When I load the URL to my HTML5 content, the iPad does not display the function bar or sidebar so there is no way to navigate the content. Any ideas?
Is your project a book file with a TOC attached to it?
Try posting the content to a web server and then accessing the files via the internet.
Locally generated files are often flagged as suspicious and will not fully load.
The files might be perfectly ok, but the browser (IE in particular) will block features.
You can make IE all comfortable with showing your local html files by adding your c:\ drive as a "Trusted Location"