I'm not sure your problem is the bell alignment, does the clutch shudder?
My guess is the clutch is not releasing properly, maybe due to adjustment.
The 3rd gear syncro's are probably worn somewhat and there are no syncro's for reverse. If it is the clutch not releasing properly it won't be too long before the syncro's for every gear are damaged.
I agree, a bell housing alignment problem is not going to pick on 1 or 2 gears. It will cause a hard shift and clutch shudder in all gears and like 67dart273 said, it will eat pilot bushings and transmission main bearing.
