Calibre can create a MOBI for you, or in the alternative you can create an ePub using Calibre then unzip the ePub (which is just a zip file with a different filename extension) and import it into MobiPocket Creator (or run the ePub "as is" through kindlegen.exe).
The point is that an ePub has a toc.ncx and Calibre will produce a well formed version of it and the .opf file.
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