The first thing to do is takes the filtered HTML and remove all the garbage that Word adds in. Make it clean code. Makes all the ToC header surrounded with h2. Take out any links to the cover. Keep the cover image separate. Use Calibre to convert the cleaned code to ePub. You can specify the cover image there. Also specify to keep the aspect ratio of the cover. See how it comes out. You can edit it from there in Sigil if it's good enough.
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