We measure our clearances from the bottom of the skirt. What we have found works best is to find different pieces of paper in varying thickness, measure with a micrometer and write the thickness on the paper. If the piston falls through it’s got more clearance. If it stops in the bore it’s about right, and if it must be pushed through it needs more clearance to match the paper.
Clearances listed below are for air cooled engines in race trim. We did have one customer that would never install his 99mm pistons with less than .006 clearance new.