Quench 318 with stock rods

Your machinist may have milled the decks to be "square" or 90 degrees from each other, but either the crank bore wasn't used as a reference, or the crank shaft was ground by monkeys. Were the rods resized?

You list two measurements for each piston is that difference fore-aft? Pistons will rock slightly in their bores. Inserting a feeler gauge between the piston and the bore at 12 o' clock should make this more consistent.

To me it sounds like the block was just skimmed. That is, it was just loaded in the machine and an even pass taken off each deck surface. The blocks left the factory cut that sloppy, and cast iron moves as it seasons, but if you're spending the bucks to do a quality rebuild it sure is nice to improve things a bit.