@egyblind:
It
might be possible to create a Calibre plugin that'll embed footnote/endnote definitions in the body text. Maybe you could ask about it in the
Calibre Plugin Ideas thread?
I've got a couple of additional questions:
1. Have you already created a couple of MS Word documents with footnote references in them that you want to convert or do you create these documents from scratch as needed?
2. What tool do you use to convert MS Word documents to epub books?
3. Did you investigate whether iBooks Author has any accessibility features that'll mark up footnote/endnote definitions so that they're automatically read by VoiceOver?