I have been running the fans in the wrong jacks for a long looong time!.. I only noticed it today cause CPU hit 80C and the alarm noise was up while fan was sitting at its puny 20% power.
Only then I noticed I had it plugged wrong; how was sys_fan2 to scale to cpu temp? lol.
But the missing bit was then, where should I plug the pump? And this thread confirmed it. As I ran gigabyte's "smart fan" bit of its "SIV" tool (system information viewer), where it "calibrates" the fans, showing rpm by workload%, I found the pump's speed informed RPM ranged about 4300RPM no matter what the workload was. I.e.:
The calibration gave a reading of 4299 RPM in 0, 10, 30, 50, 60, 70 and 90% workload settings, and 4327RPM at the remaining 20%, 40%, 80% and 100%. This means the reading the pump sends is "faked" to just indicate the pump is operational or not, no matter how the workload is input to the power jack.
Now shutting down the system to invert the plugs -- and set full speed to the connector I place the pump in. :)
I have set up alarms for stopped fans and overburdened CPUs but they never really sounded unless in extreme cases like
EDIT: in the past I didn't have issues with overheating (mostly) because I had another 12" fan in front of the radiator (so, the original fan in one side, and another fan at the other side of the radiator), and the air pull was enough for most situations. I always thought the pump picked up the pace according to workload (PWM) applied to its jack. Even if it that's the case, it seems it is not projected to that, as corsair "masks" the RPM reading to pretend it is always at maximum.
Manually changing PWM/workload to the pump did not alter noise levels.