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As always, no matter how many hours or days I search for an answer, shortly after I ask for help, I finally find it. I wanted calibre to create the NCX file for me, but gave up on that. The answer is to hand code the NCX and the OPF files. I don't mind the OPF, I just hate the busy-work of creating the NCX, since I know Calibre knows how to do it a heck of a lot faster than me.
Once you've hard-coded the TOC, the NCX, and the OPF, then you can test it by making sure Amazon's kindlegen software runs smoothly on it. However, kindlegen shrinks images and ignores pre-defined paragraph spacing, so Calibre is still required. Zip up the images, text, NCX, and OPF, open the zip file in Calibre, then use Calibre to convert to .mobi.
First bug note - The bug mentioned in the first post still exists. To replicate, create an ebook where chapters are marked with class="toc1", but have some of the tags be h3, and some be img. The images won't make it into the table of contents. (If the TOC search is //*[re:test(@class, "toc1", "i")])
Second bug note - Take a properly formed, hand-coded e-book, as defined in the body of this post. Run it through kindlegen, and it works perfectly, including setting the cover image. Zip it all up and open the zip file in Calibre. The TOC et al work perfectly, but Calibre does not recognize the cover image.
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