Hi LindsayW, and welcome to MobileRead.
The problem you're encountering re the Kindle not linking to your inline TOC in its "Go To..." menu is because the Kindle needs a pointer to the location of the inline TOC. Calibre only inserts that into the MOBI file when you set Calibre to generate a TOC from the book content - it then inserts the required pointer, but pointing to the TOC
it generated. As far as I know, there isn't any way to get Calibre to create the required pointer to point to the TOC you've already created at the beginning of the book.
You
can create a book with your own customised inline TOC and the required pointer to that, so that Kindle will link to it in its "Go To..." menu. However in order to do that, you need to create an OPF file to accompany the HTML files used to build the book, and include that in the package you zip up and import into Calibre. That OPF file can include the required GUIDE item pointing to the location of the inline TOC, which will then become the required pointer in the MOBI file, and the Kindle will link to the TOC in its "Go To..." menu.
If you don't want to have to hand code an OPF file for each book, an alternative route that you might consider would be to use
Sigil, first, to create an EPUB from your HTML files - as you put the book together in Sigil, and use the TOC editor (that creates the "logical" NCX TOC from the headings (h1, h2, etc) in the book content) and metadata facilities in Sigil, it will create the NCX and OPF files as part of the EPUB. If you keep your inline TOC in its own HTML file, you can designate that as the inline TOC in Sigil, and it will create the appropriate GUIDE item in the OPF file. Then, import the EPUB into Calibre, and convert it into a MOBI file. That way, you can use the TOC you created for the book, and also have the Kindle link to it in the "Go To..." menu.