You do not want to run a ax-5 (what's in the 4 banger) behind a 6 cyl. However, ax-15s are pretty much a dime a dozen, and they are what comes behind a 6 cyl in the yj years. You could also look for a nv3550 which is what replaced the ax-15 in the late 90s to early 00s. They can handle more power, the only drawback is most have a rattle in neutral and they take a special fluid. Also, your tcase will be easy to adapt to the ax-15. The only difference is the 4 cyl case has a 21 spline input, and the 6 cyl has a 23 spline input. These can be swapped just by changing the input and does not take much time or money.
Personally, I've helped on a 5.2 swap, 4.0 swap, and 5.3 swap. The 5.3 has by far the most power, but you'll definately have to change tranny's and tcases, and it's probably not the best option. The 5.2 definately has less power than the 5.3, but more than the 4.0. If you can find a 4.0 at a really good deal, and an ax-15 cheap, I'd go that route. You'll need the comp, and harness as well to make things easier unless your really good at wiring. They you'll need to cut the 4 cyl motor mounts off and weld the 6 cyl ones on. The only drawback to the 4.0 swap is its an awful lot of work, and can get expensive, just to have a 6 cyl. But with any swap you've listed, there are drawbacks and advantages.