headgasket was in good shape - no evidence of a leak path anywhere.
I was using a flashlight to brighten up each cylinder for the pictures, maybe that's what you're seeing? all the pistons have that carbon on them, roughly equally.
When you torque plate them they are usually a little out of round when you mic a bare block. But they are usually just little dips by the cylinder bolts. Honing them does not make them out of round. That started with the boring bar.
Where was the loosest side at? On the piston skirt side or wrist pin side? Coulda had a sleeve shoved in it after it was bored (big no no). Can cause a distortion of the rest of the cyl on that side like that. Wouldn’t cause both banks to do that though.
If the wear is on the skirt side, probably just wear and tear or like barge says, shit machine work