With a coupe, like Brian said, glass will be an issue. I would make sure you have a glass EXPERT available. If it was a fastback, the windshield could be "adjusted" as well as the back glass, to use the originals. With a coupe, it is alot more complicated.
You might want to use one of the coputer programs to modify it and see what it looks like first. With the lines of a Mustang, chopping it will make it look more lke a train than a car.
Aaron