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Any suggestions on how to go about converting it (Markdown) to epub?

Well, I went from markdown to pdf using pandoc/latex/markdown2pdf and then I think I used calibre.

However, I just tried taking one of your html files and converting it directly to epub (again, using calibre, which is free)..and it did a pretty good job.

I think if you can merge the chapters together and spend a bit of time tweaking it, you'll end up with a nice ebook.

Calibre can convert directly from markdown to epub:

  ebook-convert ebook.txt ebook.epub --formatting-type markdown
or you can use the UI.

Calibre does not like PDF. It sometimes works, but the Calibre team recommend using against using PDF anywhere in the workflow.

Calibre also comes bundled with a bunch of command line tools which, in my opinion, are much nicer than Calibre itself.

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