Adobe InDesign is the leader in the publishing industry. It's also pretty expensive and has a rather steep learning curve, but man, you can do some amazing work in it. I would recommend a few tutorials from Lynda.com:
"InDesign CS6 Essential Training"
"InDesign CS6 to EPUB, Kindle, and iPad"
"Creating Long Documents with InDesign"
I'm sure you'll learn a lot. Basically, you produce an ePub, then, if you want, you can convert the ePub to Mobi.
Alternatively, you can export the Word document as HTML and dick around in Sigil to manually clean up the code, write the CSS, etc.