The latest version of Calibre (August 2015) does a superb job converting doc.x files to Epubs. You get a perfect table of contents and better still, your text wraps around frames. Unfortunately, Calibre does not 'see' the equations, charts, and animations native to Mathematica 10. Is there any hope? Does anyone out there know of a work around?
I haven't tried using Calibre to convert docx to mobi, though I'm always using Calibre to convert eBooks in ePub, PDF or AZW.
I'm using an add-on tool in Word, free, directly help generate ePub by the document I created.