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I don't know of any way to convert direct from PDF to mobi and include a TOC. I only read text PDFs and for those I convert first to rich text font, then edit out the erroneous header and trailers and anything else I don't need, then convert from RTF to mobi.
If you wanted to add a TOC you could save the RTF as a Word doc then add in the TOC manually for each chapter, but it's time consuming and I have no idea how converting a PDF with tables would work with RTF. You might get more luck posting in the PDF forum.
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