What fluid is in the GSR tranny? When you drain it's fluid, does it look clean upon closer inspection (and bright light)?
Don't know about the clutch issue, unless you think you might have gotten oil, etc. on the flywheel/clutch face during the install.

If everything seems to check out w/ the GSR trans. other than a worn synchro(s) I'd probably keep using it since you plan on upgrading in the future anyway.