Sounds like an interesting swap. How long is the 5-speed? I'd suggest trying to keep it, run the back end of the tranny up against the torsion bar crossmember and modify the floor to match. Getting weight off the front end will help steering and handling.

Keeping the FI would be good. Can you get the entire harness out of the pickup? It may be just as easy as building a Megasquirt.

Front brakes will require some attention.
If you have more time than money you can make this into a nice car.
R.