A little more info: the <manifest> tag should probably look like:
<item href="misc/toc.ncx" id="toc" media-type="application/x-dtbncx+xml" />
but with the file name possibly different in different cases, based on the actual .ncx file name found? But here's something I don't understand: there is also a content.opf in the kindlegensrc.zip file, but it doesn't seem to match the one generated by mobiunpack.
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