Anyone have any tips on dealing with footnotes from older programs
where the footnotes are not encoded as footnotes, and easily converting
them to proper footnotes in Word?

Example would be a 50 page document with superscript numbers throughout
that represent reference's, and taking that into word and modifying /
reformatting the document so that the page layout changes, but the
footnotes, go where ever they please.

Does anyone know of any tools that can handle this type of situation?