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Have you tried simply selecting the checkbox 'Force use of auto-generated TOC'? (its under Table of Contents in the conversion settings.
If your chapter heading are in the form 'Chapter X', then Calibre should pick them up properly using the default XPATH it uses. I've seen many epubs that already have a dummy TOC with only the book title in there, which calibre won't overwrite unless you check the box I mentioned.
If the above doesn't work, report back and someone here will help you setup the XPATH expression that will work with your specific HTML structure.
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