yeah, the '00 gts manual you have does have problems for some reasons..it's most likely the synchros.
my tranny had the same problems (i also have an '00) but it went away for whatever reason. i also grinded a WHOLE lot when i put it in reverse (even when i double clutched).
i put a b&m shortshifter in my car recently though, and the grinding in reverse has also stopped now. not sure why, but maybe it's because the b&m rod isn't goosenecked like the stock shift rod?
it will most likely come back after a few months, same thing happened with my TRD
I can't explain why it does it, but the updated selector and linkage fixes the problem.