[bobcowan]

Modifying new parts is rarely the answer, IMO. Upon rare occasion, you'll find a new part that's flawed. But that's the exception rather than the rule.

Here's what I would do. Take everything apart, and fit the critical parts individually: Bellhousing, clutch disc, pilot bearing. You really need a carefull inspection and evaluation to make sure everything is exactly as it should be.

If the pilot bearing in the crankshaft hole was not put in properly, it will be slightly our of round. Not by much, like 0.5mm. That's enough to keep the trans from sliding in all the way.

The lip on the trans or the bellhousing could have a slight nick or gouge.

Also remember that everything has to be perfectly (and I do mean perfectly) aligned for it all to mesh. Get 4 pieces of all thread about 10-12" long, and screw them into the bellhousing-trans holes. Use them as a guide to slide the trans onto the bellhousing.