This looks like it is very close to what I want. Do you have a link to the sample site you are referring to? There are several examples and I am not sure which one has the organization structure you are talking about.
Shortcodes look like a winner for the headers. I had forgotten about them.
The only piece I am still a little unclear on after reading about and watching the videos on partial templates is how I can split up/rearrange the markdown content. Would I have two separate .md files, one for section A and one for section B? If so how do I access a particular piece of markdown content with a partial? Seeing the sample would probably clarify that for me.