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PDF conversion is always going to be unpredictable. You can try using Adobe Acrobat to get text or Mobipocket Creator to get HTML to run through calibre to get to epub. You might want to download Sigil as well. You can use it to clean up the various problems that will still remain with the best conversion.
You can use Sigil's search and replace function and regular expressions (regex) to try to get rid of the extra text in what you have now. It takes some study. Be sure you use more current postings as you if you try to learn about it because the particular flavor of regex in Sigil has changed recently.
You might be able to look at the current epub you have in code view and see that although the text always changes, the lead into it and out of it is always the same. That could give you a handle to locate it while searching and replacing.
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