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If you are really fond of the PDF book you are trying to convert and are willing to put in a bit of work, you could of course convert it to EPUB using Calibre, then use the freebie SIGIL to clean it up and then convert it to MOBI.
Without SIGIL you could also simply convert the PDF original to MS Word, clean it up (Find and Replace are your friends...), Save As RTF (which Calibre can happily handle) and convert it to MOBI with Calibre. All a bit like using a sledgehammer to crack a nut, but if you REALLY want a good conversion of a special book....
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