This is who I used to rebuilt my engine:
Pro-Formance Specialties - Home
They do a lot of race engines and a lot of Fords (among others). They are always busy, so it can take a little bit to get in their queue; but Matt was great to work with. The only thing is that you have to get the engine to him as he doesn't have room to store the car.
I didn't do the underdash wiring on my car, so I cannot say how easy or hard it is. However, there are detailed wiring diagram available; you can get some nice Ford Assembly books from CJ Pony. I found some brittle engine wires, so while the engine was out it seemed foolish to not replace everything. The underdash seems ok for now, plus that can be done just about anytime.
You might as well do the tranny while it is out as well. I did that myself, so I don't know who to recommend for that, but I can look up the one place I called that helped with parts, if you decide to do it yourself. I had some leaks that I figured a regular shop wouldn't take the time to deal with, plus figured I'd like the challenge.
Currently I am repainting the underneath and replacing all the brake lines and gas line. Ended up deciding to do the gas tank as well.
If your garage is stuffed, where do you keep the car?