Well, without knowing what your work flow looks like, or what you want it to look like, here are some other options:
http://code.google.com/p/epub-tools/ (includes Word file conversions)
http://www.lexcycle.com/faq/how_to_create_epub (offers a variety of options)
Several small publishers are using
www.smashwords.com to convert and distribute their books in a variety of formats. Here, again, I don't think the conversion process is customizable, so I don't know how well the results will meet your needs.
Several people have discussed the fact that the ePUB file is simply a zipped XML collection, so it may work best for your particular needs to approach it from that standpoint, use some tools to get you close and edit the XML to get the actual results you want. You might try
http://www.snee.com/bobdc.blog/2008/...pub-files.html for some ideas along those lines.
The Bandit