I am not a programmer, but I know a little (the dangerous little?) about e-book formats from reading Wikipedia.
Comparison of e-book formats http://en.wikipedia.org/wiki/Compari..._Z39.86_Format
and the DAISY Digital Talking Book (aka NISO Z39.86-2005 Format) http://en.wikipedia.org/wiki/DAISY_Digital_Talking_Book
NISO Z39.86-2005 comes in 3 flavors: See http://www.daisy.org/about_us/dtbooks.shtml
Quoted without discussion here:
1. Audio with NCX: DTB with structure.
2. Audio and full text: DTB with structure and complete text and audio.
3. Text and no audio: DTB without audio.
I think you would be very interested in #2 above as it would be a structured file (not sure if it is pdf, but it may be) of a text book that can be both read and heard within a structure for learning. TOC is basic. They have ways for a blind person to look up words in the glossary, use maps, figures, indexes, and so on.
The point is that a structure is added to the book -- the kind of structure that you need for text books so that blind and learning disabled or dyslexic students can get high school and college educations.
If you know someone who is blind, learning disabled, or dyslexic, then you can get a look at these e-books and reader free and the US government allows free postage for the delivery to the qualified person. This might be more profitable to your project to reverse engineer since they have worked out the structure needed and have been using it for years.
Believe me, the people who distribute the books in the USA are terribly careful about copyright. Check out Recording for the Blind and Dyslexic (Princeton, NJ).
Also, a student can submit their textbooks (mail them in) in requesting that they be read and formatted so the student can read the book for their school work (a two-month process). And students have been doing this for some 60 years, so that they have on file many text books for high school and college already prepared.
See also http://www.daisynow.net/core/onlineP...k/Default.aspx
This link may be a better way for you to look at some files.
Keep these thoughts on your back burner.