I have a wrecked 88 4.0 automatic. Any parts I would benefit from by swapping to my 94 5 speed?

A lot of body parts should swap. I just took a better tail lens from my non-opped 84 and swapped with my 90. Rear hatch rams. I also swapped that pin the hatch latches to. What is it, the 242 transfer case might be preferred over the 231? Idk for sure. (issues also involve spline teeth).You might want to check out the diffs. Especially the rear, you might have something cool. Seats? headliner?

I think it's the 242. What should I look for on the axles?

Boy, there's a s-load of guys here who would know way better than me. You might post again during the day with a title regarding axles. There's lockers and limited slip...just would hate to see you let something special go. I'm sure you could search it. Check the "how to search" thread above. Also there is all sorts of info there in the "info threads".

The 88 would have 3.55 gears as the manual trans came equipped with 3.07 gears. Swapping axles is an option.

A ton of stuff is swappable.

Are the differentials a direct swap?

As assemblies, yes.

How would I tell if the 88 is a Dana 44?