Will keep watching for the next video of how you solved it. I built an Auto-X before with a 200E motor, had to heat and beat a small recess into the downtube to make room for the starter, but everything else lined up. I was going to say maybe the starter is preventing you from shoving it too far forward to make room for the sub-trans, but sounds like you got it figured out.
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1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....