I just tried this myself, and yes, Calibre's header/footer removal didn't seem to work - probably some minor bug when dealing with that much html.
That said, theducks advice is good, even though your eventual target is mobi. Convert from html to epub, and then follow the advice to use Sigil search and replace. Once that's complete use Calibre to convert from epub to mobi.
Last edited by ldolse; 11-18-2010 at 07:16 PM.
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