Most metal polishes work by filling the microscopic pits in the metal surface.
These are the very pits that you need to be filled by the thermal compound, so it can't work properly if you've already filled them with metal polish.
What you really need is some proper lapping compound.
Apply this directly to the glass sheet, and repeat as before.
Ideally you should also do this with the processor, it's no good having a shiny heatsink if the surface of processor cap is like a mountain range.
I think it's been said before, but none of the above is actually lapping.
Theoretically the final process should be to match the processor to the heatsink - this is true lapping. Personally though I reckon that stage is probably a waste of time.
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