Getting the most power out of my 400 stage 6 heads

A well worked Stage VI head at 68cc has probably been milled quite a bit, so the valves are going to be even closer to the pistons than with a stock head. You are going to have to put a cam in the engine and test the piston to valve clearance. Why not test the clearance with the existing 509 first, using the STG VI heads, and see what you have to work with? Bolt the valve train and everything up and measure the clearance. That's what we do at the shop. You have too many variables to say from here, "Yep, them pieces are gunna work!"