It sounds like you have a manual transmission. Did you check to make sure the clutch disk is centered in the pressure plate when you were bolting it onto the flywheel? If it's not the input shaft of the transmission will not properly line up with the pilot bearing in the end of the crankshaft. It will hit the outer edge of the bearing instead of going into the hole in the center. That will stop you about 1/2" - 3/4" short of your goal. -- Matt

'89 4runner SR5, 3.0, auto (fun)
'93 xtra cab, dlx,3.0, 5spd (work truck)