Oh wow. What an overly complex css (in my noobie eyes).
@DaveLessnau how comfortable are you with regex S&R. You could rid the code and replace with your own in just a few S&R quite easily.
For your <section search...
Code:
\n\s\s<section data\-parent=".*?" id=".*?" epub:type=".*?">\n
and then replace with nothing
Then search...
Code:
\s\s</section>\n\n</body>\n\n</html>
Replace...
Code:
\n\n</body>\n</html>
All going well, in two steps you have removed all the <section tags