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I think Author/title information is usually stored in an OPF file. The Table of Contents is in the NCX file (but if you have one in your HTML or other input file, you can just put in a pointer to it in the OPF file's guide section and get to it from there quite easily.
I used to use mobigen and kindlegen, but now that I've got Calibre working to add the Navigation links properly, I just use that -- it lets you store larger images than mobigen/kindlegen will allow, for one thing, and has many more options.
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