So mobiunpack actually creates this kindlegensrc.zip file somewhere along the line. I just found a (slightly tweaked) version of my .ncx file in there, in the "misc" directory. The tweaks are a reflection of the directory structure.
So it looks like the changes necessary would be threefold:
1) extract the .ncx file out of the kindlegensrc.zip and place it is a (newly created) misc directory, alongside the Images directory
2) reference the .ncx file in the <manifest> tag of the .opf file.
3) add a toc="toc" attribute to the <spine> tag of the .opf file.
I haven't looked at the source for mobiunpack, to know how hard or easy this would be, nor do I know what sort of source control is being used, or where it is located.