The input shaft bearing retainer has a sleeve that the throw out bearing slides on. You have cut yours shorter. If I recall, you have it cut to about 2.25". That's a little shorter than the recommended length but it might still be ok.
When you put it back together, leave the pressure plate off. I know that it will be extra work but it will help you to be sure things will work.
With the tranny bolted to the bell, make sure the clutch disc can slide away from the flywheel. Also make sure that when it moves away from the flywheel that the end of the bearing retainer sleeve doesn't contact the clutch disc.
Then pull it all apart and reassemble with the pressure plate.
Jay
