Thank you so much. I was not aware of Atlantis Word Processor, and it looks like it might be exactly what I need, especially the "tweak_epub" utility. Thanks to this blog post, I now also understand why I couldn't open and edit the Epub I produced through Pubit; I didn't know it needed to be unzipped:
Atlantis Word Processor Blog: Tweaking ePubs: It's just a ZIP file!