you cant measure piston to wall clearance with out a deck plate.. the bores distort a good amount w/the head bolted on.

what are the problems you are having?

the pistons should rock back and forth slightly.. that is normal. Usually if something is wrong w/the piston the cylinder wall will be scored or scuffed.

 

Typically a broken piston or ring leaves a trail on the cylinder wall or on the piston itself.

Check the valves for sealing. Use fuel or mineral spirits and fill the intake and exhaust ports and see if the fuel leaks past the valves into the combustion chamber.

You could drop the piston/rod out and check it as well. I would think that any damage to the piston or rings would be pretty obvious in the cylinder wall though.