Quench 318 with stock rods

Start with having the crank indexed. Then have your rods checked out. New rods are a cheaper and stronger route. (As a matter of fact, just get new rods!) Re-fit the pistons on the new rods and assemble it with the reground, indexed crank and install. Recheck the pistons height.

If the issue still exists, bring the assembled short block to the machinist to have the block corrected.