My first concern would be making sure you maintain approximately the same intake mass flow rate. You should put a balancing damper at the furnace air inlet. When the system is balanced the damper will neither draw nor exhaust air from the basement. It will also bypass the flue if it fails to provide combustion air.
A fan might be required on the old flue pipe to induce down draft of what you hope will be warmer air. I strongly suggest putting the fan at the top, not the bottom of the flue. Air should be pushed, not pulled, for best fan efficiency.
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