Just thinkin' out loud here......but you have pressurized coolant from both heads into the manifold. There wont be much coolant "flowing through" it. To make it work better it may have to come through the manifold and then into heater core inlet,correct? In other words keep the left side as it is, and then plumb from the right side of the manifold to the heater core inlet, and block off the right head heater passage.
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