A random though, but you could use a horizontal rule (`<hr/>`) to split sections instead of the making a paragraph and filtering. They're part of the markdown syntax (using 3 or more hyphens, asterisks, or underscores) and you probably wouldn't even have to filter them out. Just use CSS. I'm actually pretty sure it's the semantic use case for them anyways. That's assuming, of course, that you don't use them elsewhere for other reasons.

Other than the unsolicited advise, I really like the workflow. I did something similar for almost all of my papers in college.