340 build

Well you won't have intake/head sealing issues with a .055" or .060" Cometic head gasket. And the Cometics are re-usable unlike standard head gaskets.

A few more parameters before you act; what do you mean bay 'standard head gasket'? The standard ones out of the Felpro gakset sets are NOMINALLY .051" thick. I don't think their thickness is all that well controlled so for tight clearance use, I would not use them personally. (Someone has reported the 8553PT's as thin as .046" thick compressed.) The Felpro 1008 gaskets are .039" thick and I think that thickness is better controlled. You have to buy them in addition to the standard gasket set.

(BTW, you can but a lower end gasket set and an intake set and save a few $$ to put towards the Cometics or Felpro 1008's.)

If you DO use the standard Felpro head gaskets (PN 8553PT, like came off of the engine) then they are nominally .051" compressed. I bet you can swap a few of the pistons around and get that tallest one down a bit. With the 8553PT head gaskets, then your pistons should be .005" to .015" above deck to keep the quench gap in the .035" to .045" range. If you use the 1008's then the number is different. If you use the Cometics, you don't need to touch anything.

Do you mean that the block will be square decked? Or do you mean that the piston tops will be milled down to equal clearance over the deck? If you ARE going to square deck the block, then count on as much as an extra .005"-010" coming off of the deck to all over to get things trued up. So, if you are indeed going to have the block square decked, you HAVE to wait on the piston work to see where things end up. Then you put things back together temporarily, (block, crank, and all pistons) and re-measure the piston to deck clearance; only then do you cut the pistons.