I don't know what you could do to change the height the piston is coming up. However the sleeve is another question. The sleeve is to be from .0002 to .003" above the block. Does yours fall in that range?
Another interesting bit of information is the block bores should be marked A, B, or C. Liners will also be marked A, B, or C. This mark should be on the camshaft side of the block. A is larger than B, B larger than C. When I say larger I am referring to block bore deminsions. Nothing to do with your question but I had not seen this before. So you guys changing liners need to remember that to assure getting the correct liners for your engines. Woe is me, my YM2002D has no liners.
Let me clarify a little more. This information is out of a service manual for a YM276, engine 3T84HA.