That's done. I finally…
That's done. I finally have a working export that produces a file looking decent enough to submit unchanged. Luckily I don't have classes that require adherence to a specific style/template (it's just font size, line spacing serif/sans-serif, but nothing major), so I just did what looked best to me.
The hard part was making sure pandoc used a reference document for the styling without having to define every time. And also setting some other prefs in a default.yaml file.