Are you making an epub3 or an epub2? The semantics set for for an epub2 html table of contents is typically the string "toc". The string "nav" is used in epub3.
If you are making an epub3, thn the NCX file is optional and can be removed. The NAV is a xhtml replacement that needs a particular structure so it is machine readable like the old xml NCX was.
Again in Sigil, your choice of where you elect to put heading tags (h1, h2, h3, ...) determines the entries in the NAV when you create it but you are free to edit those entries.
So I am still not sure exactly what the issue is other than Kindle's limit of 99 entries in a machine readable NAV or NCX but surely there is a hierarchy or natural structure of some sort that can represent what you want in less than 99 entries.
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