Hi there!
Re how quiet it is here … :-) … it's only because you're asking questions that only a very small percentage of people on the forums are familiar with. If you were asking questions about image scaling or hyphenation, then you'd probably get a ton of answers. EPUB exporting out of ID is something that relatively few people do, though of course it's picking up steam. You might get many more answers to these types of questions by also posting to forums where everyone is making EPUBs, such as https://mobileread.com. (I showed that site in my video.)
For the navigational TOC in ADE that you're talking about, what appears there is a list of links to the separate XHTML files comprising the book. If you're starting with a Book document (many INDD files in the Book panel), and you're not using the TOC/first-level option in the Export dialog box (only available w/CS5), then the navigational TOC will be the filenames for your InDesign documents. In other words ID will export one XHTML file per INDD file. The name of each INDD file will be what the nav TOC shows.
Cross-references are problematic. If you've got cross-references, do NOT rename the INDD files, otherwise you'll end up with broken links. You'll see that in the Hyperlinks/Cross-References panel after the fact, when you open a doc. Even if they're working perfectly in the INDD file/book, when you export to EPUB they may break. There is a known bug involved w/them and EPUBs, that the Teus DeJong script I show in the video partially fixes.
In my experience talking w/other EPUB producers, you'll likely have to fix the x-ref links after the export to EPUB, by making them into relative links instead of absolute ones and if you've changed a filename, to the correct filename. Knowing how to use GREP in your Find/changes and doing so across all the documents in the book will help a great deal. Or this might be something you should just job out.
Sorry I don't have better news for you!
AM