Is there a working implementation for scholarly markdown already?
You should have a glance at the latest Pandoc release.
Pandoc markdown supports almost everything you need for a scientific paper, including citations, tables, formulas etc. With 1.12 (released yesterday) there's also metadata support in the form of a YAML front matter. Pretty neat stuff.
I think we could go easily from Pandoc markdown to Lens to NLM. Maybe that's a great option for paper submission. We could have a toolchain for authors that lets them write Pandoc markdown, preview in Lens (on the fly) and submit the markdown file (or converted NLM) to eLife for review.