honda engines are known for there water pumps making a whining noise, I think they sell water pump lubricant to fix that. I would star there instead of replacing parts.

 

I have a similar problem, all the same symptoms, but only mine goes away whenever i turn the A/C on, so I believe mine has something to with the A/C, but I did just get some bottem end work done and replaced some parts too, ill see if it goes away.
-Pelon