Why would a new alternator die in a 1994 Mustang GT after less than a half hour of operation?
Recheck the wiring. If ok, the alternator can be defective. defective poor quality reman...especially if from Auto Zone.
NEVER EVER EVER buy a remanufactured electrical part from Advance. Their new (not reman) store brand ones aren't much better. If Advance is the only parts store you can get to and you absolutely have to have a starter or an alternator in your hands that very second, and a reman is all they've got,be sure to save the receipt 'cause you will be using the warranty.
Unfortunately the 2000 Mustang and 1994 Mustang are completely different body styles. The convertible tops are also different, so a top from a 2000 would not fit on a 1994. It might be possible to modify a top from a 2000 to fit on a 1994 but it would be costly and time-consuming; buying a top for a 1994 would be much easier.