Hey.. I'm rebuilding my 400. I have edelbrock 72cc aluminum heads that I don't want to spend the money to replace, and I'm buying a new rotating assembly anyway, so I have two options for bore and pistons if I want to run 93 octane pump gas. Option 1: Bore it to .060 over making it a 412 CI and use flat top pistons. Option 2: Bore it to a 461 and use dish pistons. The cost is almost the same to do either. Which will give me better performance? I've read that dish pistons don't have very efficient combustion so I'm not sure what makes the most sense to do.
Given that you have already done a price comparison, bigger cubes are always better with regards to torque & power in a Pontiac engine.
Do you have to bore it to .060 over? Would .040 work? You don't want to go any more than necessary -leaves a little meat for another rebuild. Even though pistons are generally listed at .030 & .060 over, you can typically get them at .040 over if you inquire.
I assume you are asking about the 461 CI stroker kit which includes the 4.25" stroker crank, 6.8" rods, and forged pistons? From my understanding, the dish portion of the piston is "D" shaped to match the heads, so they work well. The important thing to consider when building the engine is the "squish" - the area between the top of the piston and the head where no combustion takes place. Your machinist can get the correct clearances on this.
Another option, and I can't verify this, but can't the Edelbrock heads be machined for larger cc combustion chambers to get the compression you are looking for with flat tops? Again, maybe your machinist/builder can perform this operation and open the heads up a little more in the combustion chamber.
Pontiac's are torque engines, so I would go for Option 2 all things considered.