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You would be better of by OCR it to a Word or HTML file than an ePUB file. Then you would be able to clean up the mess better. Charts and diagrams should be converted into images. After analysis of the PDF, manually set those to images.
Don't run the whole OCR process in one go (unless it is a very simplistic book). First Analyze to see if all the areas are correct and then the read phase.
It is always better to start from the original of course.
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