Slightly off topic but I have to ask: would you be willing to share your markdown workflow for academic writing? I am very interested in graduating from latex :)
This is somehwat geared toward my specific preferences as a social scientist, but my cookiecutter template contains pretty much everything you need for academic writing using pandoc: https://bitbucket.org/jboy1/cookiecutter-pandoc-paper
You can also consult Kieran Healy's guide here: http://plain-text.co (again, this targets social scientists)
I would second this, having written a lot of documentation recently (markdown + template + pandoc -> pdf) I am very interested in improving this workflow.
You can also consult Kieran Healy's guide here: http://plain-text.co (again, this targets social scientists)