If you had the engine all apart to have the heads re-worked than a bunch of stuff was touched. You could have a problem most anywhere. Could be a vacuum leak, or valve lash, or firing order is off or a few dozen other things.

I'd start with the basics and go from there. Confirm firing order, look at the plugs, check manifold vacuum while running, run a compression check, etc. Almost anything can go wrong when you pull and engine apart and put it back together. I think I've every mistake in the book and then I find another way to make one.