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Brian - if you're happy to let Calibre create another TOC at the end of the book based on your section/chapter headings, that one will be marked in such a way that the Kindle will be able to identify it as the TOC, and the Kindle's "Go To... Table of Contents" menu link will point to it.
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Indeed, this is exactly what jackie_w suggested. The thing I mentioned is just a modification of this when you create your own toc tags throughout the book, which will be hidden and typically located just before the actual section/chapter headings (in general wherever you like have them to point to). Calibre will then build the TOC from the custom tags instead of from just the section/chapter headers.
Plus, the "Do not add TOC to book" option in the MOBI output section can be used to supress adding another TOC to the end of the book which I guess Brian may want in his case.