I am recording my thoughts about this process here because I will forget someday. Perhaps this information will help someone else.
The last two years my son’s school was offering books with a disconnected book interface. That is to say the website they were using to host to page turning books had a separate site to host audio. In the end it was very hard to for the kids and parents to use. This year they started using a new service that basically combines the two as a video. So my books aren’t being made any longer.
I took the PDF and .mp3 files they uploaded and (through a cumbersome process) I combined them into an ePub book. Each page had a separate audio player control at the bottom of the page. This was great because it made it much easier for kids to back up the audio so they could hear something again. The other huge benefit of this method is ePub files are portable, so many parents loaded their homework books up on their iPads and had them review on the ride to school!
I discovered that ePub files are an archive compressed in the ZIP format, and by changing the file extension from .epub to .zip I could view into the structure of a book. Download one of the last books from here for an example. I didn’t use any fancy software to create the books, I used a couple of AppleScript droplet scripts to speed my process (PDF2PNG, ePub_Zip, ePub_UnZip), but I hand edited the HTML and split the large audio file page by page in Audacity.
The process I used is very similar to this one by John Carroll University.
Here is an awesome video for Pages users.