Ulysses III has an awesome feature for styling RTF exports of Markdown documents. I created a .ulss stylesheet file for a double-spaced manuscript. It's still a work in progress – it's not specific to any journal's requirements currently, but it certainly could be.
Click here to view the gist containing the .ulss file (too long to embed).
Here's a sample file in Ulysses:
And here's the direct export in Word:
I haven't finished playing around with embedding figures or inserting citations. Citations are obviously huge for academic writing, and the new Papers 3 is awesome but doesn't seem to fully support Ulysses. Part of the problem seems to be that the Papers 3 popup citation inserter can't generate the references list inside Ulysses. The other part of the problem is that by default, Ulysses does crazy parsing stuff to the Papers citation placeholder tags (e.g.
I've got some work-arounds but they are too fragile to be worth writing about at this point. Even if the workflow is a little jury-rigged, it will still probably be better than WYSIWYG formatting with Pages or Word – it's amazing to have completely uniform formatting without futzing around with manually applying styles.
I'm asking for some help...we'll see what happens: