PDF files rarely convert well to .epub files. You usually get somewhat better results if you enable all options on the Calibre Heuristic Processing tab, which are disabled by default, but that's about all you can do other than cropping the .pdf file to suppress page numbers, headers and footers etc.
For more information read the "
Read this before Posting PDF Questions" sticky.
You may want to post other Calibre conversion questions in the
Calibre Conversion forum.