A stock head gasket is +-0.043" so aim for piston top at deck height and the gasket thickness equals your squish clearance. Just remove the least amount possible from the head to straighten. As I mentioned Cometic offers viton coated steel base gaskets in 0.010, 0.014, 0.020" thicknesses, (which give you options) plus MLS head gaskets in a few thicknesses as well, one at 0.040" which would be perfect if your piston crowns end up @ 0 deck.
I've never seen stock pistons as far down the bore as Cal experienced.
I would suggest whatever your pistons are below deck you remove from the top surface of the cylinder.
Don't forget you still need to measure all clearances, before you start, and after each time something is machined before you do another step. It's a process, so leave nothing to chance.