The Koolance controllers have an adapter that'll allow you to use either the smaller 3pin fan header OR a larger molex plug connector.
I missed taking the accessories picture, but you can see the adaptor/connector in the upper left here:
The smaller 3 pin female end plug into the controller and you would use the male molex plug to plug in your pump. There is just power 12V power and ground at work here, the RPM cable (If you had one), would not connect to the controller.
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