www.mustanggt.org has a great description of what changed from year to year as far as GTs go.
www.mustangregistry.org covers LXes.
The things that I think would be important for you to know is that the 140mph speedometer was added in 89 1/2, the driver side airbag was added in 90, which means you lose the tilt steering wheel, bigger fenders were added in 91, and they switched to hypereutectic pistons in 93. The 93 was the least powerful of them all, but the things that limit it will probably be changed by you anyway. It's the last year of the Fox body which may mean something some day and it would, of course, be the newest.
If you plan to just dive in and build it up right away, you can even consider buying a 4 banger and converting it to a 5.0 or even a 5.8.