Re: I want to replace my auto transmission with a 5 speed. Problems?
You will need a lot of parts off the wrecked 2000 model, but its not an impossible process.
The biggest affair is when you pull the dash out of both cars (the wreck to get access to all the pedals and such, and your car to INSTALL them).
I'd recommend discarding the OE plastic clutch quadrant and going with a nice billet aluminum aftermarket part (that old plastic piece is getting brittle by now anyway).
New parts to buy...
Clutch (you're crazy to reuse the old one), pilot bearing, throw out bearing, clutch cable, transmission mount bushings, etc.
I would recommend a nice aftermarket short throw shifter (again, the OE is probably worn out by now, and its rubbery as heck no matter what).
Swapping out the computers makes a LOT of sense (your AOD computer will be concerned when it loses touch with that AOD tranny).
I would think that you can use your existing driveshaft, but I'm not sure, so I'd grab that from the wreck as well. You'll also need the transmission mount.
Be sure to check out the manual tranny before you invest time and money in it. These are pretty weak sisters as such things go in the transmission biz - famous for eating synchros. If its about to go bad, it should have been giving your friend ample warning (particularly on cold mornings). If it needs an overhaul, now is the time to do it. Swap out the old lube for new (I'd use synthetic) regardless.
Frankly, you might be better off selling your car and shopping for the car you want. You might price all the labor for the swap with a good local garage. Even assuming you do the work yourself, it might be valuable to know exactly how much it would cost (I would say approximately half the value of the car to start with).