I am trying to convert the following book:
I have used httrack to make a local mirror. I cleaned up the table of contents file by removing the navigation links and fed it into Calibre. The chapter ordering is wrong, though, because Calibre follows the navigation links on each page. According to the FAQ entry here
I can customize the HTML to ZIP plugin to do a depth-first instead of breadth-first exploration. This will be necessary anyway because the book contains other links (like footnotes) that could through off the order.
In the plugin preferences page, I find File type plugins ->HTML to ZIP (0.7.18). Customize plugin only shows a dialog asking for the text encoding.