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Discussion Starter · #1 · (Edited)
Okay, this is like a Jeep Commander greatest hits bullet point. The leaking sun roof drain tube.


Like a lot of folks, I had this issue for a while and it was really confounding. In my case, it seemed to have been exacerbated by the sun roof frame. The tubes clogged at a point that the XK sat idle for about 7 or 8 months. Water that didn't drain managed to rust the frame nicely, and right when I got the engine replaced, that sun roof came apart. Replacing the frame was not a big deal. But I continued to have all kinds of problems with the drain tubes due to whatever amount of rust that had fallen into them, along with any dust or crud that had built up over the years.


I solved the drain tube problem by getting a roll of weed wacker line at home depot and fishing it down each drain hole, this took quite a lot of effort and patience but eventually I got both drains free. I checked the grommets at the base of the car and they were fine, a previous owner had removed those red nipples that tend to build up crap inside, so just the grommets were holding the blue tubes in place. Pouring a bottle of water into the sun roof trough at this point resulted in a loud sucking sound and a nice puddle formed under the car.


But, a couple of months later (last month), my problems returned. Okay, no problem, I'll just fish the weed wacker line back in there and wiggle it around again for good measure. Seemed to do the trick. But, in the month or so since then, I'm still getting a wet floor mat on the driver's side, or if it's a heavy storm (South Florida here), a small puddle. For a little bit there, I thought that perhaps the grommet had become unlodged and allowed the water to pour into the floor of the cabin. But, I had seen evidence of some water dripping from time to time through the pillar handle above the dashboard. I wouldn't expect to see that happen unless the drain were clogged. I tried the weed wacker line again and poured another bottle of water down, sure enough it drains and I don't see any leak at the handle area. So I opened up the trim to get at the grommet under the carpet again and it's fine, still right where it is supposed to be in order to drain water out of the frame of the car.


So I took the weed wacker line, and this time I removed the grommet from the tube and fished it upwards starting at the bottom, instead of down through the drain. It seemed like it was going almost all the way up there before I felt any resistance, maybe a little kink at some point around the dashboard area. I don't think that it was a clog where I felt the last resistance and could not push the line up any farther, but I just have no way to tell if it was a clog, a piece of rust from the old sun roof frame, or if it were butting up against any angle near the top of the drain. I started to google around more on this, because I did not like the look of that old blue tube at this point. It's like it was taunting me.


I came across this video. It's for a Jeep Grand Cherokee with the same issue, wet floors from sun roof drain tube leaks. Turns out his whole issue was the blue tubes being broken from age, heat, etc.




I'm thinking about trying to tackle this but I haven't seen any takeaparts for the Commander. I guess it is similar to his but the Commander just looks more "together" somehow. But if this is the exact same problem I am having it would make a great deal of sense. I had assumed that the blue tube Chrysler used was a single piece, running the height of the cabin, but from the looks of it, there are shorter lengths that are connected by black rubber tubes. Assembling the Jeep with shorter tubes this way would make for easier assembly in stages, but more of a problem with age as each individual piece that has to fit together now becomes a potential leak point. [Edit: After taking the whole thing apart I can definitely say your Commander will have a single blue tube, not sections.] I won't be able to get to open up anything until at least after this hurricane, but does anybody have any info or link handy on how to get at that tube? Below the dash isn't an issue as I've been in there several times by now, above the dash is more where I need to have a looksee. If I find that the XK has segmented blue tubes just like his XJ I think I am going to go straight to replace the entire length of it with a single tube.
 

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I'm not saying that you're wrong, just bare in mind that leaks that show up leaking through the A-Pillar handle can also be coming from the bolts that hold the factory roof rail in place; this is another fairly well-documented problem.

I had a leak coming out of my A-Pillar handle and thought it was caused by my driver's side door being slightly out of alignment, coupled with bad weather stripping on the driver's side door.

It turned out that a screw that was used to mount my 50 inch curved LED Light bar on the roof by the automotive electricians shop I went to, was actually too long and went through the roof, and that's where my A-Pillar leak was coming from. Replaced the screw with a shorter one and sealed the hole, no more leak.

I've also read threads about water leaking in through the roof from the bolts that hold the factory roof rails in place; over time, they can rust out and water can leak in through there, travel along the roof between the headliner & the roof, to the A-Pillar (seems to be a natural path of travel, due to the curvature of the roof & gravity) and leak out the driver's side grab handle - typically.

Just some food for thought, in case replacing the blue tubes winds up not being your issue. I have no sunroof, so, I can't give you any insight about the blue tubes you asked about unfortunately.
 

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Same here on the roof rails. I get good drainage from front and rear drains. The leak(s) I have seem to come from above the right rear door. I hear dripping in that area when driving after a heavy rain. I pulled down the headliner in the area over that door enough to find that the side curtain air bag sleeve was soaked. Not sure if that affects air bag function but I bet they weren't designed to be saturated with water. I'm going to check roof rails for sure-when it stops raining in Mississippi!
 

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Same here on the roof rails. I get good drainage from front and rear drains. The leak(s) I have seem to come from above the right rear door. I hear dripping in that area when driving after a heavy rain. I pulled down the headliner in the area over that door enough to find that the side curtain air bag sleeve was soaked. Not sure if that affects air bag function but I bet they weren't designed to be saturated with water. I'm going to check roof rails for sure-when it stops raining in Mississippi!
Sounds good @Beau's Dad; Let me know what you find.
 

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Discussion Starter · #6 ·
Okay, revisiting this almost a year later. I have acquired a new head unit and overhead video monitor to install and started monkeying around with the head liner. I haven't pulled it away completely but with the A pillar off it looks like the blue tube is not broken, cracked, or damaged anywhere that I can see. I need to pull some wiring down through the pillars so I will likely be replacing those old tubes regardless (I'm a preventive maintenance kind of guy) but looking at the luggage racks across the top I do not like the look of some of the screws I see there. So those are getting pulled off this week, reseated with non-rusty bolts and sealed up tight before I continue with the new equipment install.
 

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Discussion Starter · #7 ·
All right, having some trouble figuring out just how in the world to remove the luggage racks. I found this PDF that shows some images but... seems very sparse on exactly where to go with the trim stick to get these off. A little help anybody? I don't have the handles on the back of my Jeep, so I guess it's what they call the "applique," but... where in the world to start tugging? I don't want to break any of this plastic.

41278
 

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All right, having some trouble figuring out just how in the world to remove the luggage racks. I found this PDF that shows some images but... seems very sparse on exactly where to go with the trim stick to get these off. A little help anybody? I don't have the handles on the back of my Jeep, so I guess it's what they call the "applique," but... where in the world to start tugging? I don't want to break any of this plastic.
@HyperionAlpha; I have replaced those black pieces in the back of my Sport, with the Limited's chrome grab handles;

The black pieces are held in with pastic tabs; If you use a common screw driver & gently pull on them, they should pop loose. This is what you should see when you remove that black plastic piece;



I will warn you up front, that any plastic trim or accesories that are 12 years old, have a very real chance of snapping or breaking off, no matter how careful you are.
 

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Discussion Starter · #9 ·
I need to find Chaaz's thread and thank him. Everybody reading this forum should pull off their luggage racks for a looksee, and Chaz was right on the money. My XK was in the embryonic stage of the issue he uncovered, but I got to it well in time. Actually, you don't need to remove the luggage rack to see if your XK has this issue, but it does make it a lot easier to see, and a lot easier to fix as well.

What have we here.

41326


Paint is bubbling. Closer.

41327


Doesn't look too bad, but let's peel the seal out and have a butcher's.

41328


That's a right bastard, he's going to get ground up, bonded and painted. The rust sucks, but isn't actually the cause of my leaks. As Chaaz pointed out, that door seal is attached to a metal bar which for some reason was only ever sealed to the body of the XK with paint. Throughout most of the body this bar is tight and right on the frame, but in several areas there are one inch (or so) sections that clearly have a gap--I didn't think to get a really good photo of this, but I'll try to do that tomorrow when I tackle the passenger side. I have no leaks there that I'm aware of, but I cannot let this go after seeing those gaps. I got a 3M silicone weather stripping sealant and covered the length of the door.

Now time to tackle the bolts.

41329


This is the second bolt from the front. I started driving back the bolts from the rear by hand, but when I made it to this one I had to break out the drill because the head of this bugger was completely rusted stuck shut like a nun's legs!

41330


And here the little guy is, falling apart sitting down, treads were toast. In fact, all but one of these bolts had rust on the threads, but this was the only one that was damaged like this. I could see plenty of thread sealant had been used on the others, but it had worn away nearer the top, again on all but one bolt. That meant a trip to the shop.

41331


Yuck. Got to clean house. And I figured it's wise to add a rubber washer to the mix and cap it off with a silicone sealer.

41332

41333


This is a 6mm flanged bolt by the way, 40mm length is a direct replacement for the rusted bolts, fits perfectly. And about this point I was getting tired and the wife came calling, so I'll shop a few more photos when I complete the passenger side later this week.
 

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I need to find Chaaz's thread and thank him. Everybody reading this forum should pull off their luggage racks for a looksee, and Chaz was right on the money. My XK was in the embryonic stage of the issue he uncovered, but I got to it well in time. Actually, you don't need to remove the luggage rack to see if your XK has this issue, but it does make it a lot easier to see, and a lot easier to fix as well.

What have we here.

View attachment 41326

Paint is bubbling. Closer.

View attachment 41327

Doesn't look too bad, but let's peel the seal out and have a butcher's.

View attachment 41328

That's a right bastard, he's going to get ground up, bonded and painted. The rust sucks, but isn't actually the cause of my leaks. As Chaaz pointed out, that door seal is attached to a metal bar which for some reason was only ever sealed to the body of the XK with paint. Throughout most of the body this bar is tight and right on the frame, but in several areas there are one inch (or so) sections that clearly have a gap--I didn't think to get a really good photo of this, but I'll try to do that tomorrow when I tackle the passenger side. I have no leaks there that I'm aware of, but I cannot let this go after seeing those gaps. I got a 3M silicone weather stripping sealant and covered the length of the door.

Now time to tackle the bolts.

View attachment 41329

This is the second bolt from the front. I started driving back the bolts from the rear by hand, but when I made it to this one I had to break out the drill because the head of this bugger was completely rusted stuck shut like a nun's legs!

View attachment 41330

And here the little guy is, falling apart sitting down, treads were toast. In fact, all but one of these bolts had rust on the threads, but this was the only one that was damaged like this. I could see plenty of thread sealant had been used on the others, but it had worn away nearer the top, again on all but one bolt. That meant a trip to the shop.

View attachment 41331

Yuck. Got to clean house. And I figured it's wise to add a rubber washer to the mix and cap it off with a silicone sealer.

View attachment 41332
View attachment 41333

This is a 6mm flanged bolt by the way, 40mm length is a direct replacement for the rusted bolts, fits perfectly. And about this point I was getting tired and the wife came calling, so I'll shop a few more photos when I complete the passenger side later this week.
Great information @HyperionAlpha; Thanks for sharing.
 

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Discussion Starter · #11 ·
Okay, this thread can now live up to its name. I had a productive weekend.

41398


What you see here are food grade 3/8 inch inner diameter, 1/2 inch outer diameter vinyl tubes, and 3/8 inch inner diameter barbs to connect them. The entire reason that I am using these is for the same reason that Chrysler used a ridged blue plastic tubing: the tube is connected to the sun roof drain via a gasket that terminates in a rubber nipple. There is no sealant, tape, or anything involved. Believe it or not those blue tubes just pull right out. So with half of this 2-way barb in the new tube, we are going to stuff the other half of the barb up into the nipple at the drain, like so.

41399


You will know it fits because it'll be nice and snug. My gasket nipple was still quite supple and rubbery, the blue tubes were on the brittle side and one had split at a seam up near the nipple. (Leak!) Here's the new tube in place.

41400


Here's a shot of the path it takes to the floor. I tried to route the tube behind this dashboard frame but I couldn't manage it so I just slipped it around the side. With the plastic side cover on there is still plenty of room and nothing is kinked. In fact this is probably a preferable path because it's straighter, less chance of anything getting caught.

41401


Here's the floor end. I had a few feet left from a ten foot tube, so I just snipped it off to fit and stuck on a second barb.

41402


Same deal, only it's going out the gasket underneath the frame. I don't know about you guys but I like this being clear, I can easily see in the future if there is a clog.

41403


Here's a view of the passenger pillar, same blue tube.

41404


And a better shot of the passenger side at the drain gasket.

41405


And wouldn't you know it, just as I was finishing up it started to rain. I got to see the results of my handiwork firsthand. Passenger side:

41406


And driver side for good measure:

41407


Some notes: you will need to remove the sun visors and the forward interior lights to get at the drain gasket, at a minimum. If you have a pair of tongs or just some skinny hands then that should be all you need in order to reach it, no need to drop the entire head liner. I didn't bother securing the tubes anywhere along their path. The a-pillar frames do this job because there really isn't anywhere for it to go, and I figured that if I were to spooge things with silicone sealant, even at the drain gaskets, it would only become more difficult to work with in the future. The barbs fit perfectly to both the drain gaskts (upper and lower) and to the tubes, so I actually expect this fix should last the lifetime of the XK. Also after performing this fix, I found what looks to be a third leak point in my XK, the inner door gasket. I'm not sure if I need to seal it with silicone or if it needs replacing, but I will be looking at this closer in the next week.

One more thing, there is a lot more water going down each of these tubes than you think. It rained very, very little in the course of these photos, and it rained a lot more later that day. I actually couldn't believe how much water I saw pouring down the tubes considering just how little rain water there was, and once it really started to rain? Good night. I definitely had more than one leak point, but there is a reason that the drain tubes are so frequently brought up with Jeep Commander leak discussions. Just be prepared because you may need to go further than just this fix.

Two more things, I'm still in the process of wiring up a new head unit, backup camera and DVR, and a roof mounted TV. While working on this over the weekend I found the rear drain tubes. They flare out directly to the left and right in the rear of the sun roof, then they track backwards and move down the c pillars. It will take a lot more work to change them out but I will get to it eventually.

Here are the parts that I used in this fix.

2x Sealproof Unreinforced PVC Food Grade Clear Vinyl Tubing, 3/8-Inch ID x 1/2-Inch OD, 10 FT: 1x LTWFITTING Brass Barb Splicer Mender 3/8" ID Hose Fitting Air Water Fuel Boat( Pack of 5 ): Amazon.com: LTWFITTING Brass Barb Splicer Mender 3/8" ID Hose Fitting Air Water Fuel Boat( Pack of 5 ): Toys & Games
 

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Very nice post, ty! Would definitely be interested in seeing your procedure for the rear tube replacement as well. If you create a new thread for that, maybe you can at least link it here for people to find. Thanks again.
 

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@HyperionAlpha Excellent how-to write up! This is sure to help many Commander owners, including me. Would definitely like to see how to do the rears also. I have moved this thread to the Problems / Dealer Service forum and made it a "sticky."

.
 
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Discussion Starter · #14 ·
All right, we're back, and with this update, this thread title might deserve a change--general purpose water leak fixes, or some such, because my Commander is finally water tight.

First off, I mentioned earlier that I would take some better pictures of the plate that the door gasket sits on, as I had already sealed it up with weather stripping. I did take some photos of the passenger side a few days later but I neglected to come back here and post them. These are close-up photos but they show the secondary door gasket pulled away from the body along the passenger side of both the front and rear doors;

41687


Mind the gap! The body is warped but this thing is huge. That's going to turn into a huge problem later, but we're sealing it up.

41688


Same thing here closer to the front, along the front door. These are failure points just waiting to happen. I have read in some service postings that this plate has a baked-on adhesive behind it, it is also secured with security (star-shaped) bolts. The service manuals I have come across when researching my leak issues have been very adamant about never removing this plate, but in the event of leaks around the door, to use a weather stripping sealant to seal these very gaps. Here is one such service posting.

41689


So this looks like a known deal all along. The service advisory says to NOT remove the secondary seal retainer but to fill the voids. The diagram seems to indicate that little voids of air bubbles are the problem, but as I've already seen, so is a big-ass gap if you happen to have one. I can only imagine that this stuff may have worn away over time, if it was ever applied the way the image seems to indcate. I've seen this same service advisory for multiple Jeep models, Patriot, Grand Cherokee, etc., so it really is a wonder why it isn't talked about more with as often as a Commander owner complains about leaks. Now, we have a very interesting situation with the XK specifically. Look here.

41691


This is the drivers side with the secondary gasket pulled away. Months ago as you saw above, I spooged up the top of the retainer in an effort to stop the leaks. What I didn't take notice of before seeing so many of the service pdfs like the one above however, is that the secondary gasket retainer is not a single piece. There are actually two retainers, one that runs along the top of the door and another that runs the vertical length of the windshield pillar. There is a GAP in the retainer that the gasket pinches over, which I sealed over with weather stripping sealant so it works as a continuous hold and allows the water to drain forward instead of immediately traveling down, hitting the inner door gasket and then falling into the car at the floor.

Now for for the last--and this is the kicker that I'd been struggling with for the last three years almost.

Believe it or not, after 1. tackling the roof rail bolts, replacing them with new and getting them with locktite and sealed over with silicone, 2. after changing the forward drain tubes with brand new barbs and hoses, 3. after sealing the gaps between the secondary seal retainer with weather stripping and closing the retainer gap between the two retainers also, and 4. even after changing the sun roof gasket, after reading over and over hints from Padrimino and another user here from a few years back whose name I can't remember right now, the final and possibly worst leak point in my XK turned out to be... the windshield.

I'd read at least one post where a user a few years back said that he tried everything to fix his leaks until he happened to have his windshield replaced. He had suspected that the windshield was leaking and tried to silicone it over. Later when the guy came out to change his windshield he asked him why he put the silicone there (because he had used the wrong kind) and he told him how he'd been having leak issues. So the windshield guy told him he would add some "extra heat-treated sealant" to the drivers side and this solved his leaks. Not a lot else was said here. What is heat-treated sealant? I've no idea, unless it's the kind of sealant that a windshield is installed with. But, I've got plenty of 3M weather stripping sealant, so I started scrutinizing my windshield some more. The first thing I noticed is that the top of my windshield looked like it could have been a map of the coast of Norway. I didn't like the look of it, so I got out the sealant and a stepladder. Looking at it closer there was a gap of at least 1/3rd inch or so between the edge of the windshield and the body of the XK, so I held the tube out to the centre of the windshield and sealed all along its length back to the drivers side. Then I moved the stepladder to the passenger side of the car and did the same thing, starting inside and coming out back to the passenger edge of the windshield. I went about working on other things and let the stuff dry. After an hour or so I came back and noticed that maybe 2 inches from the drivers side edge, about 3 inches of the sealant that I laid down had fallen deeper into this gap between the windshield and the body of the car. Which meant it had to have some place to go! So I get back up top and lay down more sealant, and I kept going until it was flush with the rest of the line that I had laid earlier. I also pulled the top end of the drivers side plastic windshield cover back and squeezed a little weather sealant there for good measure. It didn't rain for a solid week and I was okay with letting it dry in the meantime, I was sick and tired of having a damp floor board so I just waited for the next squall. Once we had a good rain though, I pulled the A pillar off the drivers side and witnessed... no water at all leaking from the roof. I thought I had it licked, but the following morning the floorboard was wet again. Scratching my head, I started looking real hard at the plastic windshield cover, here.

41692


That plastic cover that you see, near as I can tell, is unremovable. At least, it appears that it is held in place by the very security bolts holding the secondary seal retainer plate to the body of the car. I would not be able to remove it without either removing that retainer plate, or breaking the plastic cover. Not wanting to do either, I thought long and hard for about... five minutes, and I pulled as much of the length of the plastic cover away from the windshield as I could, jammed the nozzle of the weather stripping tube between the cover and the corner of the windshield and body, and squeezed, running the vertical length from top to bottom. By time it dried, some of this rubber was falling out the bottom of the cover onto the hinges of the door because I had pretty well emptied the tube into that tight space. But I didn't mind that at all, I just wanted to make as sure as I could that the thing was covered without being able to see up in there. Later that day after it had dried I created a 20 minute monsoon with a garden hose and the floor board remained dry for the duration. It's rained twice since then and same story, dry floor. It only took me two years and ten months but it looks like she's water tight again. Now that I know the roof isn't leaking, I can go ahead and complete the installation of my aftermarket roof mounted monitor--I had gotten the thing over the summer but didn't want to install it until I knew everything was sealed up well because the last thing I wanted to do was to open up the ceiling to install the TV, then remove it again just to tackle a leak. This is such a relief off of my shoulders you would not believe.

Here is a link to the weather stripping sealing I used (kinda glad to have a black car just using this stuff):

 

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All right, we're back, and with this update, this thread title might deserve a change--general purpose water leak fixes, or some such, because my Commander is finally water tight.

First off, I mentioned earlier that I would take some better pictures of the plate that the door gasket sits on, as I had already sealed it up with weather stripping. I did take some photos of the passenger side a few days later but I neglected to come back here and post them. These are close-up photos but they show the secondary door gasket pulled away from the body along the passenger side of both the front and rear doors;

View attachment 41687

Mind the gap! The body is warped but this thing is huge. That's going to turn into a huge problem later, but we're sealing it up.

View attachment 41688

Same thing here closer to the front, along the front door. These are failure points just waiting to happen. I have read in some service postings that this plate has a baked-on adhesive behind it, it is also secured with security (star-shaped) bolts. The service manuals I have come across when researching my leak issues have been very adamant about never removing this plate, but in the event of leaks around the door, to use a weather stripping sealant to seal these very gaps. Here is one such service posting.

View attachment 41689

So this looks like a known deal all along. The service advisory says to NOT remove the secondary seal retainer but to fill the voids. The diagram seems to indicate that little voids of air bubbles are the problem, but as I've already seen, so is a big-ass gap if you happen to have one. I can only imagine that this stuff may have worn away over time, if it was ever applied the way the image seems to indcate. I've seen this same service advisory for multiple Jeep models, Patriot, Grand Cherokee, etc., so it really is a wonder why it isn't talked about more with as often as a Commander owner complains about leaks. Now, we have a very interesting situation with the XK specifically. Look here.

View attachment 41691

This is the drivers side with the secondary gasket pulled away. Months ago as you saw above, I spooged up the top of the retainer in an effort to stop the leaks. What I didn't take notice of before seeing so many of the service pdfs like the one above however, is that the secondary gasket retainer is not a single piece. There are actually two retainers, one that runs along the top of the door and another that runs the vertical length of the windshield pillar. There is a GAP in the retainer that the gasket pinches over, which I sealed over with weather stripping sealant so it works as a continuous hold and allows the water to drain forward instead of immediately traveling down, hitting the inner door gasket and then falling into the car at the floor.

Now for for the last--and this is the kicker that I'd been struggling with for the last three years almost.

Believe it or not, after 1. tackling the roof rail bolts, replacing them with new and getting them with locktite and sealed over with silicone, 2. after changing the forward drain tubes with brand new barbs and hoses, 3. after sealing the gaps between the secondary seal retainer with weather stripping and closing the retainer gap between the two retainers also, and 4. even after changing the sun roof gasket, after reading over and over hints from Padrimino and another user here from a few years back whose name I can't remember right now, the final and possibly worst leak point in my XK turned out to be... the windshield.

I'd read at least one post where a user a few years back said that he tried everything to fix his leaks until he happened to have his windshield replaced. He had suspected that the windshield was leaking and tried to silicone it over. Later when the guy came out to change his windshield he asked him why he put the silicone there (because he had used the wrong kind) and he told him how he'd been having leak issues. So the windshield guy told him he would add some "extra heat-treated sealant" to the drivers side and this solved his leaks. Not a lot else was said here. What is heat-treated sealant? I've no idea, unless it's the kind of sealant that a windshield is installed with. But, I've got plenty of 3M weather stripping sealant, so I started scrutinizing my windshield some more. The first thing I noticed is that the top of my windshield looked like it could have been a map of the coast of Norway. I didn't like the look of it, so I got out the sealant and a stepladder. Looking at it closer there was a gap of at least 1/3rd inch or so between the edge of the windshield and the body of the XK, so I held the tube out to the centre of the windshield and sealed all along its length back to the drivers side. Then I moved the stepladder to the passenger side of the car and did the same thing, starting inside and coming out back to the passenger edge of the windshield. I went about working on other things and let the stuff dry. After an hour or so I came back and noticed that maybe 2 inches from the drivers side edge, about 3 inches of the sealant that I laid down had fallen deeper into this gap between the windshield and the body of the car. Which meant it had to have some place to go! So I get back up top and lay down more sealant, and I kept going until it was flush with the rest of the line that I had laid earlier. I also pulled the top end of the drivers side plastic windshield cover back and squeezed a little weather sealant there for good measure. It didn't rain for a solid week and I was okay with letting it dry in the meantime, I was sick and tired of having a damp floor board so I just waited for the next squall. Once we had a good rain though, I pulled the A pillar off the drivers side and witnessed... no water at all leaking from the roof. I thought I had it licked, but the following morning the floorboard was wet again. Scratching my head, I started looking real hard at the plastic windshield cover, here.

View attachment 41692

That plastic cover that you see, near as I can tell, is unremovable. At least, it appears that it is held in place by the very security bolts holding the secondary seal retainer plate to the body of the car. I would not be able to remove it without either removing that retainer plate, or breaking the plastic cover. Not wanting to do either, I thought long and hard for about... five minutes, and I pulled as much of the length of the plastic cover away from the windshield as I could, jammed the nozzle of the weather stripping tube between the cover and the corner of the windshield and body, and squeezed, running the vertical length from top to bottom. By time it dried, some of this rubber was falling out the bottom of the cover onto the hinges of the door because I had pretty well emptied the tube into that tight space. But I didn't mind that at all, I just wanted to make as sure as I could that the thing was covered without being able to see up in there. Later that day after it had dried I created a 20 minute monsoon with a garden hose and the floor board remained dry for the duration. It's rained twice since then and same story, dry floor. It only took me two years and ten months but it looks like she's water tight again. Now that I know the roof isn't leaking, I can go ahead and complete the installation of my aftermarket roof mounted monitor--I had gotten the thing over the summer but didn't want to install it until I knew everything was sealed up well because the last thing I wanted to do was to open up the ceiling to install the TV, then remove it again just to tackle a leak. This is such a relief off of my shoulders you would not believe.

Here is a link to the weather stripping sealing I used (kinda glad to have a black car just using this stuff):

@HyperionAlpha;

There is some really good information in here;

I went ahead and amended the thread title for you, let me know what you think.

When I was searching for the leak that was caused by one of the screws mounting my light bar to the roof, I noticed that gap along the top of the front windshield that you mentioned;

I talked about it with the Jeep mechanic that I used to go to all the time back then & he recommended a type of RTV Window sealant to seal it up which was made specifically for glass, which I bought at Advanced Auto if I remember correctly.

Next time I go home, I'll have to dig it out and snap a pic of it.
 

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Discussion Starter · #16 ·
I don't know if it was the line that I laid out along the top of the windshield that did it, or if it was the amount that I added just under the top of the plastic cover, but after those two applications done on that day, I had no leaks coming down from the roof any longer. It seems nonsensical because with the A-pillars off the water that I saw seemed to be pouring in overhead from behind, but after that application my dashboard was no longer wet. The bolt recesses around the A-pillar handles would no longer "sweat" water during a rain. So the water I saw coming in from overhead at that point was solved just by doing those two things. The gap between the retainers I just sort of crafted with a popsicle stick and the 3M sealant, and after doing that and sealing underneath the plastic cover, everything has been airtight. I hated emptying so much of the tube like that without being able to see where any of it was going, but the way I look at it now, I couldn't see the leak either, so I had little to lose. After closing the gap between the retainers and sealing up the vertical edge of the windshield behind the plastic cover, there has been no water on the floor, either.

The only RTV sealant I've seen is this stuff, near as I can tell it is about the same thing, it hardens when it dries. -> https://www.amazon.com/J-B-Weld-31319-Silicone-Adhesive/dp/B00ID8F8E4
I went with the 3M tube that I got because there was more of it--also at Advanced Auto Parts.
 

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I don't know if it was the line that I laid out along the top of the windshield that did it, or if it was the amount that I added just under the top of the plastic cover, but after those two applications done on that day, I had no leaks coming down from the roof any longer. It seems nonsensical because with the A-pillars off the water that I saw seemed to be pouring in overhead from behind, but after that application my dashboard was no longer wet. The bolt recesses around the A-pillar handles would no longer "sweat" water during a rain. So the water I saw coming in from overhead at that point was solved just by doing those two things. The gap between the retainers I just sort of crafted with a popsicle stick and the 3M sealant, and after doing that and sealing underneath the plastic cover, everything has been airtight. I hated emptying so much of the tube like that without being able to see where any of it was going, but the way I look at it now, I couldn't see the leak either, so I had little to lose. After closing the gap between the retainers and sealing up the vertical edge of the windshield behind the plastic cover, there has been no water on the floor, either.

The only RTV sealant I've seen is this stuff, near as I can tell it is about the same thing, it hardens when it dries. -> https://www.amazon.com/J-B-Weld-31319-Silicone-Adhesive/dp/B00ID8F8E4
I went with the 3M tube that I got because there was more of it--also at Advanced Auto Parts.
Well you got it squared away, that's all that matters. Nice work.
 

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@HyperionAlpha I was reading up on all the sun roof leak problems and you seem to have done it all. I know what I need to do but before tearing my Jeep apart can you give some help on removing the drivers side kick panel.? I think I can do the grab handle but help there would be nice also.
Anyone else can chime in. I searched the service manuals 7,859 pages but seem to be out of luck there so reaching out for help.
Commander is an 06 and garage kept and this is the first leak.
 

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Discussion Starter · #19 · (Edited)
Glad to help any way I can, first off though what exactly do you mean by kick panel? If you're talking about the panel just beside the dash board, exposed when you open the door, all it takes is a tug with a few fingers after removing the inner door seal. A trim tool can handle it also, but there are only a couple of tabs holding that panel in place, it's pretty easy to pop off and tap back into place with nothing but your two hands. Pull from the front, as it's exposed after you remove the door seal and it'll be off in a jiffy.

The forward handles can be removed by taking a slim trim stick to the oval-shaped caps. A small screwdriver may work easier but is likely to damage the cap, it is made of a malleable rubber. Pull the cap out and the use a 10mm (I think) socket driver to remove the bolt behind it. It's very long, about three inches or so.
 

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Kick panel - the side trim on the drivers side with the hood release on it. Just want to remove stuff so I can get to the drain tube on floor to pull it out and fix, most likely also need to remove the threshold cover by door also.
Picture attached 1 is kick panel, 2 is threshold.
42964
 
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