T5 hard to shift after replacing bearing retainer

[Merlin76]

1994 GT T-5
Centerforce dual friction clutch
Centerforce throwout bearing
steel bearing retainer
aluminum clutch quadrant
firewall mounted adjuster

This is the second bearing retainer (steel) that I've had to put in this tranny since the first one came apart. The first time, I took the bell housing out with the tranny so I could replace the clutch also, but this time I only took out the tranny. Problem is, now I have a real hard time getting it into the gears...all of them. Once I do get it in gear, sometimes third gear will grind like I didn't push the clutch in all the way, and I've adjusted the clutch out far enough to know that it should be disengaged. Could the tranny just be out of alignment with the engine and clutch? If so, is there any special way it's supposed to be reinstalled or some trick to make sure it's lined up? Seems like there's not really any way of messing this part up. Or do I have other problems?
Thanks for any and all help you can provide.