Okay, I had time to mess around with it some more. A couple issues:
1: Doesn't seem to respect page breaks in the ePub (@page). I notice that my chapters seem to be all squished together.
2: The footnotes (links) feature does not respect anchors. It will get to the proper html file within the ePub, but it always selects the top.
<a href="book_split_003.html#footnote5" class="footnoteBack">return</a>
Otherwise, it's looking pretty good. Keep it up!