I would check to make sure the pressure plate and clutch are properly aligned and as noted above that the pilot bearing is correct and fully seated in the crankshaft. When I installed my engine years ago I cut the heads off bolts and slotted the ends. Then I used these as guide pins to align the trans to the bellhousing. Once aligned I replaced the guide pins one at a time with bolts and tightened them equally to draw the tranny to the bellhousing. I also had the sheet metal off The front and radiator removed which made life easier.
