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I am going to try mobiunpack now, but what tweaks are needed for the ncx and opf files? And does only the opf file go into kindlegen? Any other mobi-editing info I should know?
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That's my personal workflow and it may not be suitable/feasible for anyone else, but basically I have to recreate the ncx file from scratch (from the data in the inline TOC that will be part of the html file that mobiunpack produces), and modify the opf to properly reference the new ncx file. I also add the "start" reference in the guide section of the opf (if it wasn't already there). This is where I have some personal scripts to do most of the heavy-lifting for me.
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And does only the opf file go into kindlegen?
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The opf file is what you "feed" to kindlegen, but all of the files referenced in the opf file must be present and in the same relative location that the opf file indicates they are.
The best thing I can suggest is to take a completed (and satisfactory) epub file and convert it to mobi with kindlegen. Then take the same epub and convert it to mobi with calibre. Using mobiunpack.py, unpack both mobi's and compare them to see what epub source produces what mobi code with each converter. It's all trial and error, but it's really the only way to learn.