If you want an EFI setup form an '87-'93 Mustang, buy it. It will not matter if the computer or harness is from an auto or manual trans, you can use it either way. You need the ECU, the main harness, the O2 harness and the injector harness. It's important that the O2 Harness matches the ECU. This won't be an issue if you grab them from the same vehicle.
( The O2 harness differed over the years between manual/auto trans. the difference is a loop/return of pin 30 from the main harness, into the O2 harness and back. you can use a manual O2 harness with an auto ECU, but you CANNOT use an auto O2 Harness with a manula ECU)
Check out all the Ranger sites for swap info. other good sources are
www.fotrdfuelinjection.com www.sbftech.com and I recommend the harwood swap manual to help with wiring
www.harwoodperformance.bizland.com/
Then you need an intake manifold that will work with a 351. The only usual difference is the lower. As you've found , there are options for new parts. You can also buy used.
I have no experience with 4x4, but if I was doing it, I'd grab the motor/trans/Tcase for an F-series truck and be done with it. Likely need to play with crossmember(s), shifter holes and driveshafts, but that's the fun part.
As far as auto trans go, AODE/4R70W are computer controlled, and may not be the easiest way to go, unlees you are using a computer setup from a '94/'95 Mustang GT or a '96-'01 Explorer.
Typical AOD or C4 need no computer control.