Okay... transmissions: Your delay in shifting into overdrive is related to temperature of the engine, or actually, the temp sensor that sends that info to the transmission. Toyota made it so that you can't go into overdrive until the engine hits a certain temp. Memory tells me that sensor is at the rear of the intake in that coolant manifold by the firewall.
And swapping... basically it will swap in and work, but you may have to do a little wiring. I had a 92, and the only one that exactly matches was a 92 or 93. I've seen threads on this forum, or others where it's explained better, but during the 2nd Gen years, Toyota did some different sensors and stuff from year to year. Basically, the big stuff fits and bolts up, but electrically you may have an issue or two. It may be possible to bypass, tho. Sorry, I don't have particulars for you, only my memory of it.
The rear window... I've been fortunate to have both of my projects have a working rear window. But, I have got into them to repair the defroster, so I've manipulated the window in or out while the tailgate is down, and that requires bypassing some safeties. So, you've got switches that tell it if it's latched or not, and then if it's locked or not. That is probably where you're either going to have to repair them so they are indicating correctly, or bypass them (which I'm not sure is an awesome idea, but no judging. Sometimes ya gotta do it to get by.) I realize I'm full of help here. I have a wiring schematic from my 92 project I could look at when I'm home. But I just recently had the tailgate apart on my 95 attempting to get the damn window back up with all the rusted parts in there, so memory is real fresh.
Hope some part of this rambling helps.