Assuming that you are running a flat top piston I would think that the 427 combo would be the one to run. At 8.5 above the deck it would be easier to run higher compression and proper quench. Setting quench at .0035 to .0050 would be much easier by playing with more available head gasket thicknesses than a piston .0029 in the hole. I am no cylinder head expert but I have heard that a piston below deck usually hurts flow with a good flowing set of heads like your Indys.-Randy