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For the books I've posted here I imported the files to Sigil (for the epub) then ran the epub through Calibre (to create the mobi). It's very easy to do overall. For fanfictions that I've downloaded (I'm a Harry Potter fan) I just imported the HTML files to Mobipocket creator, built the TOC and imported a jpeg (for the cover picture) and built the book normally. Both approaches work well depending on what you want to do. This evening I saved a doc (from my 2009 NaNoWriMo project) as a HTML page, imported it to Sigil and converted to Mobi in Calibre so I can refer to my 1st draft of the book while making notes for future work. What approach you use is just dependant on what you want to do and what you have as raw files.
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