It is hard to find mustang computers at wrecking yards, though they are plentiful on ebay. The most you should pay is around $100, though you can sometimes find them for a little less if you shop around. You can go to
www.fordfuelinjection.com for a list of all the compatible computers, but among the most common are A9M, A9P, C3W, C3W1, A9S, A9L, etc. Some are made for manual transmission and some for auto so try and get one that matches your configuration.
You can use other computers but the '89-'93 mustang computers are the best understood and all the aftermarket EFI wiring harnesses are designed to use them. Just be aware that you have to match the wiring harness to the computer, so a t-bird or lincoln harness is not designed to work with a mustang computer.
Based on Ryan's last post it appears that you can have an internal EGR if you get a Lightning lower matched to a '96 or earlier GT-40 upper. Those Lighting lowers are nice but hard to find and expensive too. But on the plus side a GT-40 will flow better and get you a little more horsepower. It all comes down to what you want to spend and what combination of parts that will best meet your needs. But that's the beauty, you can mix-and-match a wide combination of different parts to suit your application.