All my front control arm bushings, top and bottom are maybe a year old. I replaced everything when I did my lift; even ball joints, tie rods and sway bar links. It's just the diff mounts that are well aged now (if you can consider 5 years "well aged"). The rears are still the original OEM stuff, except the sway bar links, but I can tell the rear is still smooth. All the new nvh is definitely from the front half, and i KNOW it's because of the new front shaft, nothing in the rear...it drove smooth on the freeway at 80+ for 3 hours just 2 days before I installed the shaft. And the jeep was parked for those 2 days. Knowing that the shaft is heavier, etc etc, I just need to figure out where this weight is finding slack to move around in....another thing is possibly having the shaft out of phase. Like how you're supposed to mark the shaft to the pinion and tcase flange before removing so you can put it back in the same position...can't do that with a new shaft. I've always wondered how much of a difference that makes, but it's still a driveline vibration term and type....so....maybe? I doubt a new front shaft would cause new nvh because of something in the rear...Oooh you got a beefy set up lol! I just got a little old 4.7 . Mine seems so sluggish anymore. Its so weird, like it has so little low end torque. I like knowing my bushings will last forever, but yep, that nvh is definitely there lol. Theirs are like hard plastic poly, when I ordered I thought they'd be like a shock absorber bushing poly, nope lol.
My vibes aren't there at cruise and coast, in fact cruising and coasting shes smooth as butter. Its under throttle the vibes show up a bit. I know that rear pinion is still off a bit, but I dont know how to get these control arms adjusted for that yet . Every since I put them in that vibration is there. You checked all your control arm bushings? Especially the rear?
I'd bet you not having your rear control arms set right yet could be your problem. You might have the rear u-joints at different angles? The transfer case output and axle pinion need to be perfectly parallel to each other.
...Assuming you didn't get a double cardan rear shaft as well (which would need different angles than the two joint shaft setup).
With new nvh causing problems over time, I found this on a Tom Woods article about Vibrations, "These vibrations, over time, will create fatigue failures. I would recommend that the source/s of the problem be diagnosed and corrected. If this is a Wrangler or TJ,.with any lift, installed or planned, one of the good tail shaft conversions (Currie), CV drive shaft and adjustable trailing arms be installed. Anything less will be simply "batting your head against the wall", expecting a summary failure that may make the conversion seem cheap by comparison. "
I know any serious vibrations will eventually wear something out, it's just a question of how long it will take and what will fail.....ugh. All the more reason I want to start figuring this out as soon as I can, which I don't have the most free time to do...I saw THIS POST by @Up4XK which doens't make me very confident about my situation, lol....😩