i put a 3" lift on my '90 XJ and had NO problems with the t-case. you should be fine and the vibes you're feeling are probably from something else like your driveshaft. climb under there and just grab the driveshaft and see if it has any play side-to-side. If it has a lot of slop replace the u-joint.
It could be. There is incredible inconsistancy in XJ's as to what lift height causes vibes and or necessitates a TC drop or SYE. there's also varying degrees by which a 3" lift is called a 3" lift (some may give just over 2", some may lift it 4")