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I have looked through the top hole and ensured the top of the fork is engaged but could not see below. This might be easier with the transmission out of the car... [/B]
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Actually, more difficult with the tranny removed, as you can't look up the bottom. I would keep the tranny where it is...
I think you missed the alignment on the fork, and then jammed it into place. You do have all of the helper spring mechanism, etc. disconnected, right? If so, the mating process should not require any tweaking, although you might have to rotate the crankshaft so that the starter gear and splines on the transmission shaft mate well.
-Wayne