You'd need some hard to find and expensive parts to keep the 3 speed manual trans in there then. I think the easiest way you could go would be to put a C4 behind it and carb it. If you want to stay with a manual, a T5 out of a Mustang would be the easiest way to go, though it's still not a bolt in swap. (please keep me in mind on that 5 speed trans )
You will need to swap the oilpan & pickup tube, the front accessory drive (everything from the timing cover forward) and replace the distributor with one from a 85 Mustang GT with manual transmission (you can buy these locally from Autozone, etc for about $60 with a core to exchange, doesn't have to be the exact core) and you'll need a bracket for the clutch Z bar mount, the classic Stang vendors sell these. Also replace the intake setup with a highrise aluminum like an RPM, Ford A321, Stealth, etc. Top it with a Holley 570 SA carb. Finally you'll need a 157 tooth 50 oz/in flywheel, if it doesn't have one already (think that one's got a 164 tooth wheel) This is basically the setup I have in my 89 ranger (but with ported heads and 1.7 rockers) Excellant setup for everyday driving, good power and fuel economy. I'd be interested in the transmission too, but you're probly too far away.
I don't understand doing away with the fuel injection and going to carburetor. Seems FI would be much better.