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Don't blame Calibre for poor PDF conversions. You need something as powerful as Adobe Acrobat, almost all of the cheap or free PDF converters are simply PDF printers. What I do is open the PDF in Adobe Acrobat and convert to rtf (you can also convert to html if that works better for you). Then I open the rtf in Word and clean it up. Novels aren't too bad and usually clean up fast. Right now I'm cleaning up a history book with a lot of inset paragraphs and pictures and it's taking a bit longer. The finished rtf will be loaded into Calibre and converted to whatever format I need. I do this so I can view the file on devices that don't handle pdf.
This workflow is for text based pdfs, image based pdfs require OCR and much more clean up. A good OCR program is essential.
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