Put small balls of plumbers putty in the pockets(to measure piston to valve).
Sounds like what you are worried about is Piston to head since you are wanting to mill, you will have to play with your cam settings once you mill it to get proper clearance. You just put the putty on the flat portion between the pockets, tighten the head down and spin the motor over. You don't have to have the rings on to get your measurement so it will be easier to put the cylinder down on your pistons just to check the clearance. Make sure if you don't have the rings on you put the putty in the front and back and measure both, and average them out because most likely the piston will tilt a little forward or backwards without the rings in there.