If the machinist swapped pistons, he probably weighted old and new to determine they are super close.
You said you got .002" over pistons or do you mean .020" over? One would require boring cylinders to 4.020" and .002" would be a ball hone.
Balancing an engine requires you to present all rotating parts to machinist at once, prior to assembly. This would be, pistons, rods, crank, damper and flex/fly.
Just call him in morning and ask, there are no stupid questions, only stupid answers.