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After letting calibre work on it for over 24 hours I gave that up. However, found a program that could convert a MOBI to HTML. Then could use Word to edit out major blocks of footnotes, cross-references cutting it down by 60%. Calibre was then able to convert the html file to epub. Then used Sigil regex to take out the superscript links. Then could use calibre editor to pretty-ize it. Then found it to be an interesting exercise but not useful as a desk reference.
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