UPDATE in OP

 

I didnt see it mentioned but you should shim the rear 2-4*. You're sitting much higher than 3". A SYE would be better of course but shims will make it much more tolerable. Without a SYE theory will say the thick part of the shim goes toward the front of the Jeep but I found at about that height shimming like it has a SYE worked much better. 2.5 years no SYE, 5" lift and nothing has blown up or folded like a taco. I had intentions for a SYE but life has dictated otherwise so I deal and it isnt bad. 90 miles round trip to work daily and in the dirt when I can.

 

I may be looking into checking my angles on the pinion. As soon as time allows. I hope this is the problem.

 

Have you checked your front DS?

I just went up one more inch in the front and I now too have a vibe over 30-40mph. After closer inspection I have a bad joint at the cardan.

I have decided to buy a new Tom Woods built to my length rather than rebuilding the one I have......for the price difference....rather have new.

 

I seriously doubt the issue is with the transfer case!
The u-joints get 'set' over time in the range they operate in. When you lift, that range changes and the 'set' can become slop or sticky movement, which will cause vibrations. Possibly aggravated by an improper pinion angle.

Vibes during acceleration can be due to pinion angle too high. Vibes when deceleration is attributed to a pinion too low.
The stock driveshaft must be equally phased, same angle at transfer case and at rear axle.

http://www.hotrodhotline.com/md/html..._harmonics.php