For example in section-5.xhtml, there are several <li>s that have text as a direct descendent. <li>s should have a <p> tag below them, even if it's just a sentence. This isn't required by the HTML5 spec, but it helps in consistency when parsing things.
Yup, though for the endnotes a quick glance suggests there aren't any with more than one paragraph. So you can probably sort out the endnotes with a regex find and replace.
For example in section-5.xhtml, there are several <li>s that have text as a direct descendent. <li>s should have a <p> tag below them, even if it's just a sentence. This isn't required by the HTML5 spec, but it helps in consistency when parsing things.