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.
If I understand correctly, the gitbook toolchain isn't freely available. Nor does gitbook address any of the limitations of Markdown that prompted me to switch to Asciidoc.
Pandoc is a powerful tool but it has some serious limitations. Nothing more sophisticated than it's own flavor of Markdown is supported. "Simple" things like internal references to anything other than headings are impossible. I had to abandon it after realizing how restricted its ReST parser is compared to the official Docutils.
But why did you choose Asciido and asccidoctor? I think Markdown together with Pandoc is capable of generatring all kinds of formats too.