Here is how I deal with MS Word documents with footnotes in them.

1. Save MS Word document as html.
2. Process using Balthasar Tidy.
3. Cut (or save) Balthasar Tidy output into a TextWrangler document.
4. Change <div id="ftn to <div id="div-ftn throughout. This will
make the <div id=ftnx> harmless.
5. Change ="_ftn to ="ftn throughout. This will make all the
footnote and footnote reference id's legal.
6. Change <a to &nbsp;<a throughout text to create a space before the
footnotes. Note, do this before transfering to the Nautilus
template, and only do it to the text portion.
7. Remove title="" throughout.
8. Use HTML Tidy in TextWrangler to get rid of blank paragraphs.
9. Change <h6>, <h5>, <h4>, <h3>, <h2>, <h1> as required. Remember
to work from <h6> up, not the other way.
10. Fix up the rest of the document normally.
--
Jonathan O'Donnell
mailto:jod@...
http://purl.nla.gov.au/net/jod
+61 4 2575 5829