I'm not sure plastigage would work considering it tends to stick to whatever crushes it but it's an interesting thought. I could try using something like lead solder which will keep its shape after deformation and hopefully not remain in the combustion chamber.
My strategy would be to set a dial indicator to the block and zero it to a plate mounted to the head. Without messing with the indicator, pull the head off, remove the gasket, and reinstall the head flat to the block. The indicator will say what the compressed gasket thickness is. Knowing that deck height is 0.021", piston-to-head clearance can be accurately calculated. Of course, this involves pulling the head...