I've been watching this post for the last week trying to decide whether to jump in, or not. I'm in. Fheyr, if you're planning to have an indy mechanic perform the swap, I hope you have a large bank account. It's gonna get expensive! This isn't a plug and play operation. There's wiring, modification, minor fabrication, troubleshooting, etc. involved. At an hourly rate it can get out of control real fast! The whole point is to do it yourself, make mistakes along the way and learn from those mistakes.
The first thing you should do is educate yourself on the workings of EEC's, electronic fuel injection and the basic functions of turbochargers. I highly recommend this book.......................
Ford Fuel Injection and Electronic Engine Control; All Ford/Lincoln-Mercury Cars and Light Trucks, 1988, 1989, 1990, 1991, 1992, 1993 : ISBN 9780837603018 - Buy.com
Once you're comfortable, give you're new turbo motor a seal-n-shine, rent and engine hoist to remove the old boat anchor and drop in the new beast. You'll have to cut the VAM (Vane Air Meter) connector off the TC harness and splice it into your existing Mustang harness. A MAP sensor can be converted into a BAP sensor simply by disconnecting and plugging the vacuum line from the MAP sensor.
You will have to repin your EEC harness connector. Once you get into it you'll see that it really is a simple procedure. Stinger has a great website but I've found one that reads and articulates very well and is complete, even down to the emissions and fuel switch wiring (if you so desire). It refers to an '85 Mustang but in reality it applies to '87-'93 Mustangs................................
Turbo Coupe Motor Swap for 85 Mustangs
With that said, I wish you good luck on your swap!