I have a few guesses:
There may be a piece of debris from one of the old water pumps that circulates through the system & "shocks" the water pump when it goes through the impeller. Flush the ^%*& out of it in every direction/orafice you can think of.
Check to be sure the cam pully is spinning true. If that is not dead straight, it can put added stresses on the pump shaft/bearing - especially at higher RPMs.
Could there be an air pocket in the area of the pump? Stupid BMW I have would stop circulating coolant unless you paid a great tribute to the BMW cooling God & bled the system, your veins, & your wallet all over the engine bay.
