there are two rods for the shift linkage. one is connected via the pin, the other is conencted using a bolt. there are also a few bolts where the shift stem is. check all those bolts.
from doing a clutch install that is the only thing i can think of that will affect you coming out of gear. it could be something internal but unless you were real rough with the tranny during removal and install that shouldn't be the case
could be something that was there before clutch install and you did something during the clutch install to make the problem more apparent.