If your water pump was going, it would be highly likely that you would see coolant coming out of the coolant weep hole, which is located toward the back of the oil pan (the exhaust etc makes it hard to see under there...use a torch).
This is a good indication that the seals (and possibly the bearings) on the oil/water pump impeller/drive shaft have failed OR are failing.
WHY?
The oil/water pump uses the same impeller/drive shaft and the seals on that shaft stop the oil and water from contaminating each other.
Another indication of coolant leaking from the weep hole is....you'll smell what i would call a sweet or odd odour (definately not an oil smell) after turning the bike off.
The weep hole is positioned so the leaking coolant drops onto the exhaust and burns off (hence the smell after shutting the motor off).
You can smell it by just sitting on your bike after turning it off as the "odour" will be coming from basically directly beneath you and it wont take long for you to get a woft of it.
If there are no signs of a leak from the coolant weep hole or any strange odours after shutting your bike off, it probably isnt your oil/water pump.
By the way...which fan is kicking in at 2000-2100rpm?
If its the cooling fan/s for the radiator, they are only operating because the motor has reached its pre-determined Hi-temperature setting before the ECU activates it.
The fan doesnt kick in based on the bikes RPM (im sure you know that) so i hope that isnt happening.
Is your motor running HOT all the time?
Its strange that the noise dissapears upon activation of the fan...there's definately something querky going on there.