Remember that too much as just as bad as having none at all. Bear in mind that it's only to fill those in-perfections so assist in the contact. However, if the IHS or the surface of the HSF block aren't level, then you may not be getting full contact between the surfaces. This is common where one core is variably higher in temperature than the others.
I would certainly look at maybe an alternative cooler just to see if the problem is with the HSF. If you have scratches, then that won't help. Filling these with thermal material won't help. Otherwise, if you think it's the IHS and you're seriously not happy then it maybe worth contacting to the supplier. Altenatively, you could consider lapping, which is the process of "levelling" the IHS but this does void any warranty. Try a different cooler first.