Yeah, 2" shackles will throw your pinion angles off horribly and also mess with the castor in the front. 1" is the most i will ever run again for a lift shackle. 4wd.com has a good deal on some 1" lift shackles for YJs. ($39 a pair)
Also if you do any wheeling you will hate the 2" shackles even after you correct the pinion and castor problems. They will hang up on rocks, stumps, and anything else on the trail. Im not telling you this because I read it somewhere, I have 2" lift shackles on my YJ right now and I hate it so I ordered the 1" shackles and a 1" body lift to get rid of them.
I say 1" body lift and some TJ flares would be a better idea. I just installed TJ flares on my 95 and its the best mod I have done to my Jeep so far.