I'm with darrsi on this one. If (i think you are) you are the same poster that recently drained what looked like engine oil out of your cooling system, have you flushed the system out yet and replenished it with the correct amount of coolant ? I would suggest this is the way forward 1st. Maybe even try a borrowed or 2nd hand water pump to try at the same time as i imagine it wont have done yours much good having that gunk circulating around in it ? I know you have stated that you have inspected the water pump and all looks to be ok but as others have said, it could well be the source of your mystery noise.
Yamaha Fazer 'the only bike you'll ever need' maybe ???