I have 6603 cranks on two of my bikes, both of which run 10s Ultegra cassettes and chains. Installing a new chain and cassette on either bike means perfect shifting and consistent cog/chain meshing all through the cassette range.
Without seeing the bike or hearing the noise you're describing, this suggestion may be way off, but have you checked that your derailleur hanger is straight? Indexing a cassette to perfection with a bent mech hanger is pretty much impossible, even if the hanger is only slightly out.
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Matt
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