I'm just using the pad that came attached to the heatsink/fan combo. Simon, I must say seeing as your upgrade heatsink/fan and Artic Silver paste comes in at ball park 200% more than the bog standard version, I would have expected you to achieve lower temps than my setup.
I have checked the temps tonight since I connected the intake fan, and the temps are CPU 44 System 33 as against 45 and 33 last night. So as one assumes the same room temp, the additional input fan has made very little diference. On the face of it not worth the extra time and effort of drilling holes and the addtional purchase cost. But having said that, the fan does blown incoming air directly onto my hard drive, so I dare say it will insure it stays cool.