Your never going to be able to drop the t-case enough to stop the vibes. About the only way your going to get rid of them is to go with the CV driveshaft. Trust me on this one....I spent many many hours trying to get rid of the vibes with shims and t-case lowering kits.....And I only had 3" of lift.
Yep -mine is only dropped an inch. I don't have any vibration either - when I set up my D44 in the rear, I changed the pinion angle to match and also had new shafts made because the D44 has a pinion housing that's about 2" longer than the stock Model 20 rear.
2" is too much. I have no problems with clearance (running 36" tires).