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The problem with checking the ends of the cylinder is that most oblong wear tends to happen more in the center of the bore. I knew the chance of it being out of round was minimal given the lack of miles on the motor, but the debris scuffing on the cylinder walls was pretty severe. I agree with Jerry about honing it a bit more until those vertical scratches are gone. They aren't very deep looking, so your piston clearances should still be ok. They are usually loose on an aircooled engine anyway.
As far as the piston, yes, that is a good way to check them for any taper wear.
I would definitely take the time to clean the heck out of that cylinder. I usually clean with warm soapy water, and then wipe down with clean rags and WD-40 until I get nothing to wipe off on the rag anymore. Then coat the cylinders with a thin coat of assembly lube (it sticks better).
This would be a good chance to try and flush out the crankcase and clear the centrifugal oil filter as well. Might as well start with as clean of an engine as you can.
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