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I suggest trying the Kindle book in Windows MobiPocket Reader (I assume you have a DRM-free version, just change its extension from .azw to .mobi). Most likely it will be fine "as is". If the Kindle showed the TOC in its menus then so should the MOBI version. If the TOC isn't listed under the "Contents" icon, then perhaps you should produce a MOBI-specific version but there are hundreds of MOBI files with only an in-lined TOC (no TOC under contents) and these are perfectly acceptable for most ebooks and may be better in some cases. If an internal TOC was best for the Kindle then it may be best for MOBI too in this case.
If you want DRM, then unfortunately a .mobi file can't be imported into MobiPocket Creator and so you will have to build a new ebook from the HTML (use the .opf if you have one). If the TOC is in-lined then this should be easy.
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