how to measure piston to cylinder tolerance, and piston ring gap

Yamaha XJ 900 engine with 100.000 km on the clock, burns oil on cylinder 1 and 2 I suspect that it is the valve stem seals that has gone hard over time, and because of that, oil can leak through the valve stem into the cylinder 1 and 2 when the bike is parked on the side stand. but since the engine top end is disassembled, I thought it would make sense to check the cylinder, pistons and rings