i currently own a 98 wrangler sport, stock 4.0, 5 speed and am thinking of swapping out the tranny for an auto since most (99%) of my time is in town. any suggestions on which would be best if i also install 4.6L Golen stroker? Am actually looking to add performance to the box so any suggestions on axle/gear would be helpful also.

I'm in the same boat as you.

the availible 3speed auto turn a wrangler into a dog.

my plan is to keep an eye out for a cherokee (the grands have a different tranny thats supose to be weaker)to act as a donor, build that engine into a stroker and swap everything (stroker engine, tranny, computer (compuer controled tranny), and t case too, diferent input) out at once.

I've saw a writeup on putting a 700r4 in there, might actualy be easier, but I know the aw4 works good with the 4.0
http://www.rockcrawler.com/techreports/aa_autoswap_yj/index.asp

they also have other good writeups too, including a stroker build