Yes, it sounds like you have a rod knock. I don't think you can remove pistons from the bottom- unless the crankshaft is out of the way. And 'yes' to cutting the ridge from the cylinder to remove the piston, as 3B says.
If indeed you have a rod knock, the crankshaft is likely to be damaged, so you need to check that crankpin carefully with a micrometer.
Harvester
