From your description of your progress so far -- converting the PDF to Epub but having formatting issues and not having access to all of Epub's features -- is probably as far as you're likely to get without substantial human effort.
If you want in-depth information on format conversions, etc., and advice from people who do a lot of this, you might consider joining the forums at Mobileread
. (I'm not trying to "pass you off," and hope this sort of referral doesn't run afoul of Bleeping Computer.)
After introducing yourself, check out the forums on E-Book Software and E-Book Formats, especially the Workshop section. People over there tend to be knowledgeable and helpful. If there are tools or procedures to automate this process there's a good chance someone over there knows about it.
(Disclaimer: I've been a member over there for more than a year but I have no connection to or interest in the site.)