His .002 sounds reasonable.
I agree with tlowe. The pistons you’ve described sound like those available off the shelf – for example:
Egge 270 GMC which call for .002 clearance. As for the variations you’ve mic’d don’t forget to divide those measurements by two. If the largest piston is .001 larger than the smallest one – it will tighten the clearance by .0005 on opposite sides of the bore. Same with the bore variation.
Let’s review the arithmetic just to make sure we’re on the same page. Stock bore is 3-25/32 inches or “3.78125. 30 over would be “3.81125. An off the shelf 30 over piston designed for .002 clearance should therefore mic at 3.81125-.004 = 3.80725 somewhere low on the skirt (just as you described – perpendicular to the wrist pin) typically some set distance from the oil ring groove.
What are the measurements of the largest and the smallest pistons?
What are the measurements of the largest and smallest bores?
The solution during the build may be as simple as rank ordering the pistons from largest to smallest – and similarly rank ordering the bores from largest to smallest – and then putting the corresponding piston into the corresponding hole . . .