In the Electrical section someone once asked how to wire a Mod Motor to a Fox. I responded, "First, mix a good stiff drink." Not a bad idea..... All kidding aside, here are some suggestions.
Get a good multi-meter that reads resistance (ohms) and DC voltage. Some years ago I got one at Radio Shack for something like 15 bucks. Good investment. Then get the Electrical/Vacuum Troubleshooting Manual (EVTM) for both the donor car and the receiver car, and plan on spending a lot of time studying both. There's a link on
www.foureyedpride.com to wiring diagrams for Fox Mustangs. Thanks to a low friend in a high place at Ford, I have the 1998 Shop Manual and EVTM on CD.
Taken as a whole, the wiring system can look very intimidating, so break it down sub-system by sub-system. Take one sub-system at a time and trace its entire path: for instance, start at the battery, follow the starter circuit thru the ignition switch, out the dash, into the engine bay, to the solenoid and the starter. Do the same for ignition, lights, horns, instruments, fuel pump, etc. Determine where the connection points will be between the car and the engine wiring. And WRITE EVERYTHING DOWN! The good news is Ford is fairly consistent with circuit numbers and wire color codes so it's not hard to figure everything out, just tedious.
Good luck, keep up posted on how you're doing, and don't be afraid to ask for help. We've all been there a few times.