You can do the key dance to pull the codes yourself, but it will only display the PCM codes, which are just about all the OBDII mandated fault codes. It will NOT display codes from other modules or extended manufacturer codes, like for Body and Radio Modules, which seems to be your problem.
Well, on a positive note, at least the dealer looked your vehicle over and gave you a list of everything they could find wrong for the $105 diagnostic fee. For many Dealers the $105 diagnostic fee is for hooking up the Chrysler proprietary scan tool and downloading the stored fault codes ONLY. Yea, five minutes work that anyone can do, except Chrysler saw to it that only the Dealer can practically do it. Although it does sound like the Dealer went on a fishing expedition to run up as many charges as possible, to try to get you to pay for.
I think it is the Mini-Vans that have a TSB for the AC system, causing condensation dripping into the radios and amplifiers, someone correct me if I'm wrong, I don't think this is a problem with Commanders. Sounds like you electronics are more along the line of results from water from the leaks, except the original complaint.
A cracked coil could cause stalling, if you were getting stalling without any other symptoms, and the PCM would likely store a code you can pull up yourself with the key dance if that was the case, the new coil may have fixed that. If your were getting stalling when all the displays in the interior of the veicles flashed and shut down, then that is likely the root of the problem, NOT one of the coils.
One last thing, for info, with my AutoEnginuity Tool, with the Enhanced Chrysler Module, I can run all the tests and activate individual speakers and the amps, even with the radio off. The whole radio and amp is "computer" digitally controlled by module in the vehicle. So, my "Guess" the water and shorts from it, is cause signals that is doing all sorts of weird things to the module that controls the Amp.
Oh, and sealing leaks, keep in mind spending a few extra bucks to a fair amount of money on a professional is worth it. Just grabbing a tube of leftover home caulk may NOT do the job, or fail a few weeks later and you'll have to do the job again.
If your roof rack is leaking into the interior, what I have done for similiar; things like spoilers, roof racks, etc often have studs coming out of the bottom that goes through holes in the roof. The seals fail and water that gets under those items on the roof leak right in through the holes for the studs. You have to pull the headliner, never an easy tasks and actually remove the roof items, clean everything up and then put a bead of sealant in a circle around the stud and reattach the hardware.
If you have a bad seal between a none moving window and body, the best way to fix it is to take it to a professional and have them remove the window and put new sealant in with the window.
Best way to get RTV and other sealants to seal, clean surfaces of course, also keep the time between putting the bead down and re-assembly down to 5 minutes. Longer than that, the RTV or sealant start to cure and does NOT adhere to the surface well enough to make a good seal. Visit your local auto store and look at all the sealants and RTV's, select the one that seems most applicable to your needs. But for sealing out water between two body parts, the basic black RTV seems to work just fine, that is what I have used. Home Caulk may NOT stand up to the heat, UV rays, salt and road chemicals a car experiences, I would use RTV over anything that does NOT specifically state it is for use on "Automobiles".