Im going to be swapping out my ax-15 (manual 5 speed) for a aw4 (auto 4 speed) Mine is a 93 yj so it will be a little different. It can be done. Its not that hard just pretty involved and be ready to do some re wiring. I've heard that it is well worth it though. Here is really good link with a TJ tranny swap.
http://www.stu-offroad.com/engine/aw-4/aw-4-1.htm