,
When you installed the clutch, did you align it?
I have found when mating the two, leave the trans in gear, with the engine at the same angle as the trans, slide the two together, if/when stopped, turn crank a little to get the engine to mesh with the output shaft. This usually gets the two within 1/4" to 1/2" of each other, where you can then use the bell housing bolts to pull them together.
If you have the engine mounts installed, you may want to remove them to give yourself more clearance until you get two together.
I highly recommend that you DO NOT use the bell housing bolts to mate the transmission to the bell housing. The transmission and the bell housing should mate almost completely flush with each other IF the tip of the shaft on the transmission has been inserted in the pilot bearing and there is nothing binding.
That's just my opinion - it may be worthless.
Gnarls.
