ez's have a raised intake port and stock location exhaust port. indy extended the intake flange a little to allow for a stock manifold.

So stock type manifolds will work on this combination?

I am planning my next engine build. It will be a 512 stroker using a 400 block. I have a set of Indy EZ heads. I've had them about 10 years (bought new and never installed on an engine). Are the Indy EZ heads from that era taller than an Edlebrock head? This engine is going in a 68 Charger/Auto and I want to use the stock hood. Also, whats your opinion on these older heads? Would they be as good as a modern Eddy or 440 Source head?? Thanks

Since it is a 400 block you should be just fine. The Indy heads move the intake up but a 400 block is shorter so you probably end up in the same general location as a factory RB block.

Your other question on EZ heads vs. other heads is tougher to answer. I'd say that if you're going to run standard port heads then the Trick Flows are the best option. But you would need to sell the EZ heads and buy the Trick Flows so I'm not sure you want to do that. The EZ heads work great when opened up to MW size. As a standard port head they aren't great since they are really a MW head with a plug of material at the face that necks them down to a standard port size. But if it is just a street car they'll work just fine. Like I said, not an easy decision. Since you're building a 512 you could open them up to MW size but then you have to run the 400-2 intake which is fairly tall. Nobody builds a low deck dual plane MW intake which is what would work great on your car. You could get someone to modify a Performer RPM to fit on MW ports but it would cost some bucks.