The gray material is most likely thermal paste that helps conduct great from the cpu to the heat sink. Maybe in taking it apart you dislodged whatever was making the noise?
That Patina is the Thermal paste getting contaminated. I would order a whole new thermal kit from Newegg.com Toss the old one. You can also order the Silver Solder Cleaner and Silver Solder from them.There's also green corrosion on the copper backing of the pump. Does that indicate a leak? Joed, the sound is coming from inside the pump, not any of the fans. This is what I found surprising in the first place.
What is the best way to remove the excess thermal paste?