When should you adjust the overall pickup height (of a covered humbucker btw) and when should you adjust the height of individual polepieces?
Also how should i change the height of a bucker to get a less muddy, clearer sound?
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Adjusting polepieces is for changing the balance of the strings. Adjusting height keeps the balance the same but just makes it louder or quieter.

I don't think it has any significant impact on note clarity.