Mike, when I said to rotate the cylinder with respect to the piston, I meant independent of the crank -- out of the engine, if possible.
I'm assuming that this engine still has a ball and socket joint instead of a wrist pin -- right? I have both a TD 09 and a Medallion 15 where both the cylinder and the piston are out of round. This works fine when the ovals match up, but when the piston's big way is aligned with the cylinder's small way, they jam. Since the piston tends to rotate in a Cox, the engines won't run for any length of time.
If yours has this problem, then you're probably out of luck unless you can find a new piston/cylinder. If it has burrs, as Kennith suggests, then his solution may fix things.