For the last PDF book I converted, I used the Poppler Utility
pdftotext with the
-layout and
-nopgbrk options, cleaned it up in Jstar, my text editor and moved it into LibreOffice and saved as ODT. Then I just used Calibre to convert it to ePub. Worked out pretty well.
I use Linux, but the Poppler utilities are available for Windows as well.
http://blog.alivate.com.au/poppler-windows/