This is a socket 775 cooler, right? Do you have any experience installing these coolers and applying thermal paste? I still think your cooler isn't mounted properly
If I were you I'd unhook it, remove the mainboard, put the mainboard on something soft (IE: Cardboard)Clean the CPU heatspreader and the heatsink with cleaning alcohol and reapply the thermal paste. Make sure that you wipe the alcohol off with a lint-free cloth otherwise you'll scratch the polished metal.
Inspect the CPU cooler for damage and mount it according to instructions.
But it'd probably be better to have someone with more experience look at it and judge your work.. Or possibly do it him/herself.