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There are only three things sealing in the compression - rings, valves and head gasket. Valve guides have nothing to do with sealing compression unless they're so bad the valve doesn't rest on its seat. So it can only be one of those three. By the way, Pete Roper recommends .005 and .007" for round fin engines and a thousandth less for square fins. No point in hammering the tappets. As for the compression loss - a leak-down test seems like the next logical step. If nothing else, create a fitting to hook a compressor to the spark plug hole and give it 100 psi, then listen for the leak - exhaust pipe, carb, sump, or head gasket.
You are supposed to remove the rings, and insert them one by one into the cylinder using the piston to keep it square when checking. It's not unusual to have to file the ends to get them within spec. You were lucky if it didn't score the cylinder.
...... we were just more careful this time, it’s working as expected. Go figure.