I was reading this post because I suffered from a mystery noise also and it turned out to be the Harmonic balancer. Your problem does not sound like it's the balancer but if it turns out to be the water pump it would be a good idea to replace the Harmonic balancer also. Your in there already and the part is pretty cheap, and likely more reliable then the factory installed one.
If the balancer fails at highway speed it could do a lot of damage... so much so that you better hope you're still under warranty because your talking about much $$$$.