See here about the rust;
http://www.lcool.org/forum/viewtopic.php?t=831
Agree, also check the chrome strips at the third row seating under the outside chrome strip. You'll need to remove the interior trim in the rear cargo area to get to this. Water will make it's way in there through the pins that go through the body work, a big dab of roofing silicone will fix that. Water will also make it way to the quarter panel from the bolt(8mm nut) that holds the black plastic vent trim on that is at the third row seat rear window glass. Another place it can get in is on GXL's the plastic quarter panel trim, just above the rear bumper wrap around. Pull the bung plug out of the panel, it is found just behind the rear Mud Flap on each side.
The oldest 80's have celebrated their 21st birthdays last year, so if they have never been checked for water and let out, it could be a problem. I have also read that in the front sill channel, were the wiring loom runs can have water sit in it as well, I haven't found water in mine and I don't know where it gets in.
Sorry this doesn't help with your Gear box question, My old girl is a manual and I don't really know about the Autos.