Nice work!
To control the motor, I would use a small controller like you said. I used a Kelly KDS72100 (72V/100A) controller to control the field current in the original SepEx motor in my car. It never let me down. However, these small controller are only available up to 72V, so I'm not sure what you would do about that.
[EDIT: Oh right....you will probably build your own!]
As far as controlling it goes, the original setup is simply an ECU triggered relay that switches the A/C clutch on. I would use the same relay, but instead use it to switch the TPS circuit in the A/C motor controller. Set the controller up so that an open circuit (or high resistance via relay pin 87A N/C through a resistor) in the TPS circuit is 0% throttle and a closed circuit (ECU commanded "clutch engaged") through an appropriate lower ohm resistor in the TPS circuit is 100% throttle.
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