For those curious about the process: making the EPUB and Mobi files was excruciating. I'm currently working on a project that should make it much easier in the future. Stay tuned.
Thank you for your work and I'm particularly interested in your publishing process. I've been asked about making ebook formats for some of my HTML-based writing and have basically said, "that sounds waaaay too complicated"
This isn't a direct solution for you since your material is already in HTML. But LeanPub[1] is one simple way to get ebooks. You write in Markdown, and they produce pdf, epub and mobi formats.