Fix up User Guide index page/Table Of Contents

Added a title so that the index page doesn't render with a title of "<no
title>"

Limited the TOC to 2 sections deep to keep it from getting too big.

Removed explicit naming of the sections from the index page. Sphinx
picks up the section titles automatically from the headings on the
content pages themselves. Allowing it to do so will help keep the TOC
up-to-date in the event of any section name changes.

Removed the cover image as this wasn't being displayed on this page
anyway (it is on the Introduction page).
Not Orphans

Don't need the :orphan: metadata field as these pages are all included
in the toctree.
User Guide error, warning, and typo fixes