I also put on 2" spacers over the weekend. I had slight vibrations while accelerating in 2nd and 3rd gear only. I dropped the skid only about 1/2 inch and that took care of that. I also put on 31" tires too.
If you dont feel any vibrations, you don't need to drop the transfer case.
Yes, dropping the transfer case does change the angle of the engine and transmission also.
1999 Sport, 4.0 5 Speed, 2.5" RC Lift, 1.25 body lift, MML, JKS Quicker Disconnects, Super35, 4.56 gears, Ected locker,33x10.50x15 BFG KM2's
2014 Rubicon, 6 speed, Teraflex leveling kit