I am surprised to see the mobo specs say there are only two fan headers- CPU_FAN and SYS_FAN. You say the PUMP is plugged into CPU_FAN, and the RAD FANS are plugged into the only SYS_FAN header (presumably using a Splitter). So do you have NO CASE Ventilation fans at all, other than the air brought in by the rad fans? Are you sure the RAD FANS are plugged into the only SYS_FAN header?
Anyway, the Manual I could find shows virtually no info on fan header configuration options. So this will be what is common, but may not match yours exactly. Go into BIOS Setup and find the configuration screen for the SYS_FAN header. Set its PROFILE to "Normal" or "Standard". Check carefully the choices for MODE. They will be PWM Mode, Voltage Mode (aka DC Mode), and possibly Auto. Set to PWM Mode. Now look for the choice of temperature sensor. Set that to CPU, not MOBO.
While there, go next to the CPU_FAN header. Make sure it is set to PWM Mode also, so that the pump will get a constant full 12 VDC and run full speed all the time as designed.
When you've made your setting changes, use Esc back to the Main Menu, then F10 to get to the Exit Menu. There choose to SAVE and EXIT to save your settings and reboot. ALL the fans should start at full sped briefly, and then slow down for a cool system, but NOT stop EVER until you shut down. If things do not go that way, post back here what you do see.