Hitting the sway bars is normal for a lifted XJ, the sway bar relocation brackets are a good fix as long as your sway-bar disconnects still fit.
I cut a slit in my XJ's brackets, bent them up and welded the cut up.
You might want to get a pair of no-lift shackle relocation boxes to adjust the shackles to a more favorable angle.
http://www.hdoffroadengineering.com...oducts/no-lift-xj-shackle-relocation-brackets
Don't bother with playing around with the shims yet, do the SYE and get it over with. It only takes a couple hours to put it in and it can be done with the transfercase still in the vehicle.
Lift the Jeep as high as you can and put it on stands for access. Look for a writeup, it takes a pair of snap ring pliers and sealant for resealing the case.
Expect to spend many hours getting everything adjusted and aligned, it's all part of the game and enjoyment.