HELP!! need experts advice on 440 trouble.

If the heads or decks are cut, you also need to cut the intake manifold. Make a simple drawing for illustration. Draw the front of an engine with heads and manifold on. Draw a centerline down the center of each head or down the port face. You will see that lowering the heads on the centerline (cutting) actually brings the heads closer together and they move downward. The manifold become too wide for the new angle, thus riding higher on the intake ports.

The actual difference might be very subtle, depending on how much was cut, and the bolts might actually line up somewhat, but if the heads are ported and gasket-matched, a misalignment would affect flow across the mating surface.

Maybe one of the engine builders here could better explain this.