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My advice would be to start fresh with Sigil, a free and excellent software for building epubs.
Personally, I have no patience for Word. I simply run the Word doc through word2cleanhtml dot com online, open that CLEAN html in Sigil, add my own style sheet, split it into chapters and sections, and build a book that really works. Takes time, but all good things take time. Automagical fixes are usually pretty awful. (You can of course tame Word, but I would rather devote the time to actually formatting the book as I want it to look.)
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