Couple things. As mentioned a thicker head gasket could be your answer.
As to your question how much was the block cut. It isn't really the right question.
Your machinist is right that the twisted block would require taking more off one end than the other to bring the deck in parallel to the crank. Likely needed more of one side of the deck than the other as well if twisted.
The real question is what is the new deck height? You need this measured from the crank centerline. I wouldn't assume the guy did anything wrong unless that measurement is off between ends of the same bank or from one bank to another.
I would also want to know why the positive deck height of the pistons was higher on some cylinders than others. Did your machinist assemble the short block or did you? Who measured the rod length and piston compression height? Was the crank indexed? I would suggest swapping a couple piston and rod assemblies from the same side IE the .040 proud one for a .034 proud one to see if that would bring the heights closer together. Entirely possible that tolerance stack of parts could be the difference and not anything that the machinist did wrong.
Another possible solution would be to run a set of the 340 edelbrock heads that have a chamber relief cut.
If you are going to have to cut pistons for valve clearance anyway you might want to shop for pistons instead at that point. Get a newer lighter piston with narrower rings rather than spending money on the old used TRW heavy pistons you have to cut deck height and valve clearance.
