You're right, it only has one CPU fan connector. You need to get a PWM fan cable splitter and run both the radiator and the pump off of that. Running the radiator fan or the pump off anything else will cause issues. Running the pump off of a case fan header is inadequate, because as you say, the motherboard temps are low and case fan speed, specifically, power to the case fan headers and thus anything connected to them, will be slow as well. Since the motherboard and GPU temps are low, speed to the pump is not increased in proportion to the CPU temperature or if using the case fan header for the radiator, then radiator fan speed is not being increased in proportion to the CPU temps.
Just to test the theory, if your cooler came with a 4 pin molex adapter, use that to power either the pump or the radiator fan and connect the other to the CPU header. Retest temps.