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Calibre is, in my experience, a bad tool, especially for this kind of a job. Sure, the fan boys will bash everything in their way and it happened to read around here at least a couple of times that the fault is with the document at hand and not the bad converter.
My solution is to use Abbyy Finereader. It's quite cheap compared with the Adobe pack and it does a wonderful job of reading even old Xerox machine quality docs. But Abbyy is bad at outputting stuff. So the latest version (11) can save as epub, but it would be filled with mistakes. One way it would be to help it by going through the style editor. Another way would be to fire Sigil and fix it there. With some basic knowledge of HTML you can solve those issues fast.
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