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Facepalm - you're right, my regexes got a little too aggressive. I've reposted it with the formatting intact.

I also posted a version as PDF - again it has the linked TOC which makes it easier to navigate. The PDF isn't as nice as the HTML though.

Do you have code handy to convert from html (with a TOC) to epub?

I looked up some python examples to start with:

I made this one with Calibre, and its optimized for the iPad. Let me know how it looks for you.