I wrote a short book recently [1] and went through a similar process. Started writing using Markdown & Pandoc but soon realized that Markdown isn't a very good fit for longer technical documents. As an example, support for asides aka admonition blocks is nonexistent. I switched to Asciidoc + Asciidoctor and the process was much more productive.

[1] Python for the busy Java Developer. http://antrix.net/py4java