Performance building with a SBC would include setting the squish (the dimension from the piston crown to the underside of the cylinder head, with the piston at top dead center and the head gasket in place.) Most everyone will agree that the squish on a SBC should be between 0.035" and 0.045", so you measure your "stack" of parts before you begin your build. You use the radius of the crank stroke (half the stroke), so on a 3.48" 350 crank, the radius would be 1.740". Add that to your 6.000" rod length and you have a 7.740" stack so far. If we agree that the nominal block deck height of a SBC block is ~9.025", then subtracting 7.740" from 9.025" tells us that we can use a maximum piston compression height of 1.285" before we begin pushing the piston crown out of the hole with a stack that is too tall for the available block deck height. Now, don't misunderstand, it is acceptable to pop the piston crown out of the hole by a few thousandths if you need to make up for a very thick gasket and reach a desired squish. Let's say for instance that the block had been surfaced before you got it and measures a block deck height of 8.990", but you need to use your 9.000" stack of parts in the block. Assemble the motor with the piston popped up out of the bore by 0.010" and use a gasket thickness of 0.050". This will put the squish at 0.040" and everyone's happy.

Back to the 7.740" stack that we had. If we were going to build a high-perf motor, we might choose a forged, flat-top piston such as this Ross example, with a compression height of 1.268".
Ross Racing Forged Pistons 95465 - SummitRacing.com
Adding that figure to the partial stack we had earlier will make a completed stack of 9.008". Again, with a block deck height of 9.025", that leaves us with a piston deck height of 0.017" (with the piston at top dead center, it lacks reaching the top of the bore by 0.017".) Now, with any other SBC block, there is a variety of head gasket thicknesses available, but with a 400 block, composition gaskets start at 0.040" and go thicker. If we are to have a nominal 0.040" squish, then we must cut the block decks to zero deck, the sum of the stack, which is 9.008".
With a block deck height of 9.008", a stack of 9.008" and a gasket of 0.040", we will have a 0.040" squish and all is right with the world.