Well I finally got around to taking my PC back apart. I took out the ThermalRight Ultra 120 Extreme and My Q6600. I had bought some 600 grit and 1500 grit paper, and also had some 150 and 220 grit that was lying around.
I looked at a few guides and they are all about the same. Use a flat piece of glass, start with a coarse sand paper and work your way up. Some suggest using water, some said oil, another one said don't use anything. I just did all of my sanding dry and it seemed to work fine.
My Q6600 seemed to have a concave shape where the outside of the IHS was the first to start showing copper. The TRU was very convex and the middle of it showed copper very quickly, and it took a long time to get it sanded all the way near the corners. It took me a lot longer than I thought it would to sand it down, about 3 hours total for both of them. The longest part was getting the nickel (Silver stuff) off. I would suggest definitely starting with 150 grit sandpaper that is decent quality. I think the stuff I had was more for wood than metal, so it didn't seem to sand quickly. The 600 grit and the 1500 grit worked better and gave a nice smooth finish. I don't have a digital camera so sorry but I didn't take pics. One more thing that is noteworthy. Be careful when sanding the processor as you'll start sanding your fingers as well. I ending up putting tape on the end mine fingers after my thumb started bleeding.
So the end result... I fired up Prime95 and I can definitely tell there is a drop in temps. I don't have any reliable data as I didn't do a baseline before, but I do know it was at least a 5C drop if not more than previous times I've done it. I hit about 46C loaded where I'm pretty sure I've gotten near 60C in the past. (Can't directly compare though because I'm not sure if that was at the same voltage and clock speeds)
One thing that I do know for sure is that the differences between all of the cores is much closer. It used to be cores 0 and 1 were always 5C higher than cores 2 and 3. Most of the time now Core 0 is 1C higher than Core 1, and Core 1 was about 1C higher than Cores 2 and 3. So it's usually 2C - 3C between all 4 cores, and they can get to within 1 degree of each other.
Overall I'd say it was probably worth it, but if I do it again I'm going to get some better 150 grit paper and hopefully it will go faster.
Now I need to see if I can OC higher