Brian,
I think the 3spd and 4spd autos are the same length so the tcase will stay in the same spot and the 2dr driveshafts should be good to go. I might be wrong, but I'm pretty sure the hole for the tcase shifter is in the same spot for all trannys (manual or autos).
The harness swap will be a PITA ...
There are subtle differences in even the dash/instrument harnesses that may require pins changed (or swap those harnesses too).
I believe the body harness (lights/fuel pump/etc) will mate right up (but that rear defroster won't function
). If the 4dr is going to a scrapper, then I'd cut the body harness plugs in case you need them to swap the ones in the 2dr body.
My books are still packed away, but I have the "supplemental" electrical book for the '91, possibly the same for a '93 (covers the 4dr differences).
P.S. keep the '91 dash