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AFAIK the Calibre crew's working on a better PDF input for their conversions, but due to the nature of the format it's not an easy task.
If you don't mind making some of the corrections yourself, you could convert to something you can edit by hand (like RTF), fix it, and then convert that to ePub, but it's a lot of hard work if it's something, for example, you'll only read once.
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