Probably the easiest way to generate an epub document is to use pandoc.
By using this combination, you get many powerful things built-in.
One of the questions around the interface between old and new technology is that of page numbers. Should an ebook need to have page numbers? Why? This is a matter of debate For academic purposes, a mechanism to point to the source of an idea or quotation is important, and so I would suggest that some kind of reference system is needed.
In the case of paper books that is the page number and the way in which you can get a page number into your epub has been set out in the guidelines: http://www.idpf.org/accessibility/guidelines/content/xhtml/pagenum.php