You'll not be able to measure the clearance properly without pulling it apart. What did you set your ring gap to?
The cylinder is very likely ok. If there's any evidence of a nip then it'll probably clean up with a bit of acid and a quick hone.
Fontyyy would use that piston again, and in dire circumstances it's probably ok.
Blimey, my old TZR125 didn't bed in properly with race pistons until at least one seizure and a rub down
