I did a 4age Swap in my AE82 sedan. I had an FX-16 donor car with a rotted out body, but good motor that I used for the swap. It's for the most part the same stuff you have to go through when you are doing a 4ac to 4age swap in an AE86. You have to swap over all the wiring (Dash, engine harnass, lights, etc) and all the mechanical stuff in the engine bay and run an additional fuel line if you're gonna go EFI. The hardest part I had with the swap was the Fuel Pump Sending Unit on my donor car was rusted out and it took me months to find another one in a junkyard in Florida. Granted, you could go with an external fuel pump, but thats up to you.
As far as the tranny goes, I went from a manual to a manual, so I gues you would have to change all the linkage and what not over if you're going from auto to manual.
BTW, Here's the finished product: