I am pretty sure the door shell is different and I know the regulator goes in a different spot for the wider glass. The sheetmetal around the area of the mirror and door handle is different, so they probably redesigned the whole inner half of the door shell.
Not 100% sure on this. I'll try and remember to compare when I'm at the junkyard tomorrow morning. I do know that people have put 97-up doors on an MJ before (jp magazine had a writeup on it) and they just had to move the door latch strike post on the door frame a bit, so there is a good possibility you can just swap 97+ doors right onto the rig and gain 97+ mirrors at the same time. Not sure how the interior trim will play with being swapped from a 96-down onto a 97-up door, can always leave the 97-up trim with the caveat that the glovebox will not fully open with the door closed.
EDIT: if you just want to get rid of the vent window you can swap in solid windows there, not as good as eliminating the small window portion entirely but it'll stop the leaking and wind noise at least.