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Converting PDF files is difficult because it all depends on how the original PDF was created. I don't think there's really any easy way to do it without having some touch-ups necessary on the finished product. Are you converting to ePub? If so, you may want to use Sigil to clean up the finished ePub.
There's also several other threads here on MR where users have developed a system for their conversions that seem to work. Try looking for those.
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