Is it just one remote that stopped working? If so more than likely it is the remote's battery. If both remotes stopped working, sounds like they lost there code. The simplest diagnosis is to just buy new batteries and install them in the problem remotes. If that does not work here is the process of programming them as long as the GT's process is the same as other post 97-98 Fords, which is:
Insert key into ignition.
Alternate switching key from ACC to OFF several times until you hear the solenoids click. (approximately 8 times)
Once you hear the sound leave the key in the ACC position.
Now depress one button on one remote only one time.
Now depress one button on opposite remote only one time.
(while depressing buttons on remotes the door lock solenoids should react and either unlock or lock, depending on which button you pressed)