The biggest problem is the shorter drive shaft. Even with a slip yoke you can end up without enough length to keep the shaft in the seal and on the output shaft. On the street no problem but when flexed on the trail it may come off or be stressed enough to break.
The brake lines can be moved a little at the front Anitcanman has a great picture how he did it. You will have to jack your rig and check droop on the fronts and rears to see the impact.
89YJ 2.5L TBI, AX-5, NP231 SYE, Ford 8.8, Yukon Grizzly, Tom Woods Shaft, 33" BFG T/As, 4" lift, Warn VR10000s.
AF Jeep Club Tail #184