Assuming you are using an AOD or c4 trans, and not a later AODE or 4R70W.
You can use any year V8 Mustang harness, '87 to '93.
You can use manual or auto, it won't matter, there is no transmission control done by the computer. The computer itself can be from a manual or auto, will not matter.
The harness is three pieces: Main harness, injector harness, O2 harness.
There will be slight wiring differences based on the original trans in the donor car. If the harness came from a manual, wire it like a manual. This is in reference to circuits 30 and 46, and dictated by the O2 harness.
Here's a handy manual for reference.
http://www.fordfuelinjection.com/files/M-12071-C302.pdf
As far as the tans harness goes, I kept my Ranger one attached the the 42-pin connector. You truck has a different style of main connector(s) than the '95-later trucks, though. Anyway, I just hooked the stock Ranger trans stuff to my T5 (VSS, reverse lights) It was very straightforward.
If you don't have it, I recommend purchasing the Harwood swap manual (Google Harwood Ranger). It will walk you through this step by step.