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The only accurate way is to install the pistons and measure from the deck of the block down to the piston dome. I put the engine together , take this measurement then take the motor back apart and take the block in to cut this amount off the block. I like to zero deck my blocks.
Two identical engines except for the deck height the one with zero deck height will put out a bit more power then the other one.
Only problem with zero deck height.......if the need ever arises for a rebuild down the road, and the block needs another decking, you're at your limits. I like the piston to be .002 in the hole...yea, you give up a little bit of power, but in the scheme of things, the power loss is chump change, plus you have a safety net for another deck cleaning, should that need ever arise.
What is .002 for a clean up? My pistons were .032 on one side and .030 on the other. I had the block decked that amount. As for increasing the piston to head clearance I could always use a thicker head gasket. I run .040 copper gasket with .040 stainless O rings.
If you you have to use a thicker head gasket, that negates the benefits of a zero deck height, doesn't it? If you leave room for future clean up, and are able to use a thinner gasket....anyhoooo....like anything else, 10 different people, 10 different opinions, and not one of those opinions is wrong, just personal preferences.
We build all our racing engines with zero deck height ,but of course if we need a cleaning up , nothings usually left.Both ways work ,We use diff head gaskets all the time to compensate for comp& cam changes.Above posts is a fine way to ck deck height.