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I've been fooling with editing the input stage of the debug output, and wrote a perl script to modify the html files to put header markup with class="chapter" around the anchors the toc.ncx file points at, then I do the conversion matching h1 through h3 headers with class=chapter and tell it to force replace the TOC. This works nearly flawlessly, and leaves me even more confused about why the manual says the convert will use the existing TOC if the file has one. All I've done is move the existing TOC into the html, so it should be the same.
Anyway, this does seem to solve my problems, and the few errors left appear to be actual bugs in the original doc which I can fix by hand.
Next I need to finish my script to convert all the opaque grayscale .jpeg files into .png files with transparency so they'll look natural when you change the background color.
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