New to the forum, signed up just for this thread. I don't have a solution unfortunately, but my situation is uncannily similar.
'03 TJ, Regeared to 4:56, brand new Tom woods front driveshaft, replaced axle shaft u joints, pinion yoke, ball joints, rebuilt t-case with new chain, new transmission mount, MC adjustable front lowers, Teraflex super short SYE with an Adams driveshaft turning an ARB locked 8.8 in the rear.
My vibe starts around 65. Below 65 it's smooth. Goes away when the front driveshaft is removed. Had a tiny bit of play in the front t case output, rebuilt it. Had the stock ds balanced and rebuilt, then replaced it Had a tiny bit of u joint play on the front pinion yoke, replaced it. Bad tranny mount, replaced it. Front pinion angle is within 1° of the ds, vibe doesn't seem to change much with change in angle.
I'm planning to pull the front axle back apart and double check my backlash, tooth pattern and pinion preload sometime in the next couple weeks just to rule it out.
There seems to be a million threads on lots of forums describing similar vibrations with no solutions. Hopefully we can figure this out someday.