Is the bottom of the bellhousing open? If so, assemble the trans onto the bellhousing with just the clutch disc on the shaft, no pressure plate. See if you can spin the disc freely with the tranny in neutral when the trans is bolted up tight. That should determine if it's clearing the flywheel sufficiently. If not, grind the back of the disc spline, or extend the tranny shaft spline further back. If the bellhousing is not open at the bottom, try turning the disc through the starter hole.
Jerry
