Crazy as it sounds it will evac quicker but the heat will be higher because the fire is burning more efficiently. Your right in your RF theory you just engineered it wrong. Move the stack to the fire box side and plug the original hole or buy a stack from CG( their like 15 bucs)and install it on the FB end and don't extend it. if you elect to stay with the 1 stack narrow the RF plate by 2" 4" out from the fire box. Enough heat smoke will escape to eliminate a cold zone in the middle. Keeping it fairly well equalized, If you add the holes in the baffle it will be very stable and responsive to small intake damper changes.
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