If you're going to mill the heads, one needs to measure the piston crown height at TDC on BOTH cylinder banks. Frequently one side will have a different height than the other. I always shoot for .040 to .045 of quench . . . really helps improve the performance of a flathead.
Also, depending on whether or not you have a high-performance/high-lift cam, you'll want to measure the valve clearance at the top of the valves (where the eyebrow section of the chamber resides). I like to have about .060 over the valves (or more) - this is on the TOP edge as the valves are canted and the top is where they are most likely to have interference with any particular head.