Atlas T-Case Vibration

I have a 92 XJ, 4.5" lift, recently installed Atlas 3.8:1 T-case and swapped stock Dana 35 for a Chrysler 8.25 with 3.55 gears. Have a high frequency vibration coming up through Atlas shift levers worse during acceleration mainly 3rd, 4th and 5th gear (manual transmission) and a whine as speed increases when in low range. It is NOT the driveshaft, the pinion angles, or anything on the front end. Could axle wrap cause this?? Anyone put an Atlas in their XJ??

Make sure the atlas is clearanced enough at the floor pan. I would assume you are getting drive train vibs from contact of the case to the floor.
Sort of defeats the purpose of the tranny shock mount if the T-case is in contact with the unibody.

Atlas is clear of body and crossmember vibrations are ONLY coming trough the shift levers, Atlas manual says that would be pinion angle, however I have tried every different angle possible with no change, starting to think tranny problem but wanted some other feedback.