Try using the Atlantis Word Processor for any future writing which needs to be converted to EPUB, it's supposed to be VERY clean. It should also do a good job of cleaning up the code if you open an MSWord doc and resave with Atlantis -- how well this compares to MSWord's filtered html setting I haven't got a clue, because I basically know this from Google+MobileRead lurking, but it could be worth a try.
Or try using Open/LibreOffice, which tends to output cleaner code to begin with, and has the
Writer2ePub extension, although I believe this achieves its wonders by ignoring tag soup and assuming there isn't fancy weird stuff in the document. Again, try opening, in LibreOffice this time, saving as a native .odt and then using the export tool.