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PDFs don't convert very well--they aren't designed to be ebooks and don't really contain the right information.
One thing that sometimes works for me is to open the PDF in Microsoft Word, which will offer to convert to a Word document. If the conversion completes, look at whether it looks OK and save it as a docx format.
Then let Calibre convert the docx to epub--it does a very good job in that regard.
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