Yep, approximately 3/8" from the bottom of the skirts.Are you measuring piston to bore clearance at the right part of the piston?
Perpendicular to the pin, a little distance up from the bottom edge of the skirt.
I almost exclusively run 100LL AVGAS, or 100 sunoco unleaded from a local station. Though with 9.5:1 when it was a 650 I never had any preignition issues even with standard 93 octane.I'm now puzzled, those bore dimensions are standard size Morgo, so have not been rebored. On the piston clearances you have, things would have to be really hot for the pistons to tighten, as it appears they have. What fuel were you using? The "standard" compression ratio with a 0.039" head gasket is 9.5:1, very high indeed for US fuels
Unless the pistons were overly tapered to begin with. Perhaps poor ring bedding and loose clearance prevented adequate heat transfer. I'm at a loss.