Dear Kovid,
Thanks for your help. I believe I have corrected the html toc to be listed in the guide section in the OPF
Code:
<guide>
<reference href="Text/Rights.xhtml" title="Copyright Page" type="copyright-page"></reference>
<reference href="Text/Title.xhtml" title="Text" type="text"></reference>
<reference href="Text/Cover.xhtml" title="Cover" type="cover"></reference>
<reference href="Text/TOC.xhtml" title="Table of Content" type="toc"></reference>
</guide>
I don't see spurious Table of Contents entries in the ncx, but I'm not exactly sure what they would be, so

. I should note that there are chapters in the book that have their own tables of contents, and their entries in the real table of contents contains the words "table of contents", but that shouldn't have anything to do with this.
(Side note: The Edit Book feature is AWESOME! Thank you)
So here is a part of the TOC.html file in the epub
Code:
<div class="sgc-toc-level-2">
<a href="../Text/numerical-discourses-book-threes-fool.html">I. The Fool</a>
<div class="sgc-toc-level-3">
<a href="../Text/numerical-discourses-book-threes-fool.html#sigil_toc_id_1">3:1 (1) Peril</a>
</div>
<div class="sgc-toc-level-3">
<a href="../Text/numerical-discourses-book-threes-fool.html#sigil_toc_id_2">3:2 (2) Characteristics</a>
</div>
And here is the same part in the azw3:
Code:
<div class="sgc-toc-level1">
<a href="part0007.html#6LJU1-b6266d1d9bb1475c93532ee14823c3f2">I. The Fool</a>
<div class="sgc-toc-level1">
<a href="part0007.html#sigil_toc_id_1">3:1 (1) Peril</a>
</div>
<div class="sgc-toc-level1">
<a href="part0007.html#sigil_toc_id_2">3:2 (2) Characteristics</a>
</div>
You can see that the sgc-toc-level-2 and sgc-toc-level-3 have both been changed to sgc-toc-level1
I guess what I keep not understanding is why the TOC.html file would be treated any different from the other html files since I already have the toc.ncx.
Thank you so much for your help and all the work you do with Calibre.
I have put the new files here along with the job record
https://www.dropbox.com/sh/dnprfnbvf...dAu3hAeCa?dl=0