yes, you are right - .039" of thickness will make a difference...
you would ideally want to check it without a gasket for several reasons, one, you know if it clears withouth a gasket, that it will clear with one, and two - who wants to compress their gasket, and completely torque a head down - just to take it off... so, it's better to do it without a gasket.
I'd be looking for about .080" on the intake side and .100" on the exhaust side. This is because the exhaust will heat up more, and if you ever run into float on the extended life of the engine, you dont want chance meetings out there (in the 50,000 + hard miles range)
Now, it's not necissarily the cam size or valve size that determines Piston to Valve clearence. The duration and lobe seperation has alot to do with it, because the exhaust valve will not close before the piston is TDC at the end of the exhaust storke - and the intake valve is opening too, and there in lies 99% of clearence issues. so - bottom line - different cams, different heads and different pistons (even in stock blocks the specifications may vary) all will result in different clearance numbers, so its always good to check.
you can put a minute amount of clay in the valve depressions and cut them in half with a razor after you have very carefully pulled it off the piston and measure with micrometers. or there are other ways
i cut my pistons(i used to run a rediculas cam before the TFS stage 1), doesnt cost that much - but another thing you can do if your engine is not only together already, but also in the car, is buy smaller rocker rollers
hope this helps
