Whats the exact deck height, and what is the CH of your piston??? Your using a stock crank and rod I assume?
Cutting the pistons is not a big deal however it is less common with a stock style build up. With a factory 3" stroke, 5.03" rod and a 1.60CH piston and a nominal 8.200" deck you are usually anywhere from .007-.010" in the hole STOCK.
If the pistons are sticking up .020" and they need to cut another .005" off to square it up I would worry about the deck thickness of the stock block personally since they are all over the place. I have never had to cut a stock 302 block that far...
Like mentioned above keeping the quench area in the .035"-.041" range is ideal.