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There are no "good" PDF conversion tools, because PDF is a terrible, terrible format. The best luck I've had is with Calibre, and it requires tweaking settings for each and every PDF I convert (line-unwrapping factor, header and footer regular expressions, chapter detection, etc) and half the time I still have to manually edit the output in an epub editor like Sigil in order to get chapters sorted out correctly.
Stay away from PDF "ebooks" unless you have no other alternative.
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