We did one at work last year, from what I can remember you need:
1) cut/weld new motor mounts (obvious)
2) 4.0 tranny
3) 23 spline input for t-case (or 4.0 tc)
4) 4.0 fan shroud and possibly power steering reservoir, among other accessories like air intake
5) 4.0 ecm (watch out for SKIM)
As far as wiring goes it was basically as simple as adding 2 injector wires to the harness IIRC, since your 2.5 uses a distributor you should be fine in that department (wiring wise). HOWEVER, a couple years ago I was wanting to do the swap on my '00 4 cyl and ended up just buying a cheap 4.0 truck. I personally wouldn't waste my time doing the swap when a v8 is not much more difficult and certainly not any worse on fuel than the 4.0 (plus more power). No matter which swap you choose I would highly recommend having a complete donor for the swap, not piecing **** together.
good from far, far from good.
'99 TJ frame-off rebuild: http://jeepforum.com/forum/f22/99-tj-frame-off-rolled-bold-1199954/