*Update* I figured out my supposed syncro problem; it was rather stupid. I had the screw on the shifter screwed a little too far, which wasn't allowing 3rd/5th to go in all the way.
well my first gt, which was a 98, had the same thing happen to it right at 36,000 mi. with the exception, that it was second gear. i don't think it has to do with anything you have done to it. more of the fact that it has been beat on a little, or a lot depending on how you drive everyday just cut your losses with that one & get a beefier one when the funds allow it