I would think that if your carb venturi, (the smallest part), is actually .406" as you say, that should be a large enough carb and you could run it. I'm not familiar with this engine, but one thing for sure, if you rotate the cylinder you will HAVE to rotate the piston as well. The rings on the piston are pinned so as not to rotate and allow the rings to pop out into the exhaust port. If you rotate the cylinder and not the piston, the rings will be in the incorrect position. The pistons are also usually machined a little differently, with a little more clearance in the exhaust port area because of the higher heat there. You will also want to look things over carefully to see if the transfer port passages in the cylinder will line up either way with the crankcase.

Good luck,
AV8TOR