could be your synchros but have you tried installing speed-sources shifter cable bushings speed-source
? they improve the feel by replacing your rubber bushings with solid versions.
if you do take it in the service advisors may blame the shifter but federal law, magnuson-moss act, prohibits them from denying service. magnuson-moss warranty act
they have to prove that the aftermarket part caused the damage (a short shifter shouldn't be the cause of bad synchros either). the problem i see you experiencing is having the service techs duplicate the problem.
mine is sporadic, also (even after installing the shifter bushings; just less frequent) but i'm gonna try and hold off until i install a quaife lsd, lightweight flywheel and new clutch plate and get them checked/repaired at the same time.
STILL, if i have to i have proof of the problems BEFORE i installed my b&m s/s.
whatever happens, though, good luck