Head milling

Pull the heads and cc but even then it doesn't mean they weren't milled at an angle on some belt sander at the local carquest.
Your going to have to take them to a good shop and have them corrected, sad thing is they might want the rest of the engine to figure it out how bad it.

It sounds like not only is manifold sitting high but the angles way off.

And if you decide you can live with it with more silly cone then put a small bead across/below the intake ports keep from vac leaking in the future.