I believe 93 - 99 were high pinion and non center axle disconnects (same as your XJ but not your TJ) but should bolt right in both. Just make sure the new axle has the same gear ratio as the one it's replacing.
I had this once a while back. There is a box built into the tub behind the inner fender. Inside it is some type of vacuum or emission box (I didn't look it up to see exactly what it was, maybe someone else can help out) that had come loose and would knock when turning or over bumps. I removed...
A 2" body lift will be fine. I've been running one on my TJ for 10+ years. Never had a bolt come loose, break or get "stressed". They are a cheap simple way to gain extra tire clearance. Good luck with your decision.