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If you're making your mobi with Calibre, there are a few complications, the answers to which I'm not sure of, but here goes.
First, you'll need to tell Calibre not to add it's own Table of Contents because this ToC functions like the toc.ncx. That is, Calibre calls it a metadata ToC. If your epub has a toc.ncx, then Calibre makes its metadata ToC from this toc.ncx. Since your NCX has all the entries (h1, h2, etc), then the metadata ToC that Calibre makes will have them all as well.
So when you convert, in the "Mobi Output" section, check "Do not add Table of Contents to book".
Additionaly, your internal HTML ToC needs to have a pointer for it in the <guide> section of your OPF file. That creates the proper entry in the display when the Menu button on the Kindle is pressed.
Something like this:
<manifest>
.
.
.
</manifest>
<spine toc="ncx">
.
.
.
</spine>
<guide>
<reference href="filename.html" title="Table of Contents" type="toc"/>
<reference href="cover.html" title="Cover" type="cover"/>
.
.
.
</guide>
</package>
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