it looks as though the PO hacked it up a bit, based on the pics. if I were you I'd try and find a new wiring harness in a junk yard or online and put it back as close to stock as possible, then modify to YOUR preference. Who knows what has been chopped out of there. did you run the codes yet as suggested? that might help lead you to what's missing...
its a sweet looking car though. definitely worth getting back together the right way
That's my thinking.
I'd source out all the original equimpment, including the power steering and the a/c, i'd bet with the way things are done there that they just capped a power rack. make the car appear to be a stock mustang.
If wires are cut on the harness, just get another harness. Sorting it out is more trouble than it's worth.
I know it all may sound terrible, but it isn't going to be too hard to make that car right again.
Proper harness
Some bolts brackets, hoses and accessories.
That's about it, nothing that will really cost much money.