Not knowing specifics of the setup, it sounds like you are altering the driveline angle causing wear and premature failure.

With my Jeep I have had to drop the transmission/transfer case and raise the height of engine motor mounts to keep driveline angle near stock.

Yup the driveline angle is definitely different but since the new pinion flange is closer to transfer case by 1" the yoke now has better engagement on the output shaft. I know the angle is slightly more steep from that but I have good news. The bushing I linked is the exact ID and OD we want but longer. It allows for the full length of the yoke to be inside of the bushing and lubricated with oil because of the little oil channel spirals. I put a new seal and the new bushing in yesterday and there is absolutely zero slop and it got rid of driveline noise and vibration.

Unfortunately I do still have a bad wheel bearing or the caliper slides don't move well enough on one side, so I am still getting roaring from the back right side, but the center roaring and flopping around/vibration is all gone. I can't really expect too much from junkyard stuff but I'm probably just going to swap in more junkyard stuff to save $. Already tried sanding down the slides and the bores on the calipers but they were pretty rough.