Is this Fixed-Format?
Regardless, choose your problem: horrifically mangled OCR spew, or improperly-converted sidebars.
Either one requires fixing by hand.
Alternatively, Kindle Previewer might be able to do directly from DOCX to dual-MOBI and preserve everything, and KindleUnpack can extract an EPUB from that, which *might* do the trick (or a trick, anyway).
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