One thing that I do a lot of (And I'm probably pretty lucky here as my workplace has a copy of Adobe Acrobat Pro) is saving PDF's as HTML 4.01 with CSS. I then use html2lrf to convert for the reader and the result is very good. There have been a few times that I need to clean up the Adobe rendered HTML (Adobe really likes to use SPAN's - sometimes to the point of rediculousness).
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