Manifold heat control valve replacement?

I recently bought a new Dorman exhaust manifold (…) Don't have any dilutions that the new manifold is going to function properly without significant re-work. I had to machine my manifold to bring the ports into the same plane. I also had to modify the exhaust box flap very significantly to make it even move freely!

This what you describe is not even close to normal. You got a severely defective manifold—should've returned it in exchange for another. Most people who buy the dorman manifold have no trouble bolting it on and going on with their lives.