There's a long thread around here about PDF, but I can't seem to find it right now.
It's hard because not all PDF's are created the same, but in general I've always gotten the best results by using Acrobat Pro to dump the PDF contents to HTML (assuming it's a text based PDF not image based) or using Mobipocket Creator to dump to HTML. Then create an ePub (and clean up PDF to HTML problems) in Sigil or Calibre editor.
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