Design the data format (API) first, then the user interface later. You have the cart in front of the horse.

Rather than decide how it looks and works, decide how you want the data structured then come up with a format to represent it. This sounds like unstructured to minimally structured document centric data - something like a Markdown with additional tagging or an XML format would probably be ideal.

This way, eventually when your design changes or someone wants to shift the data into another format (say mobile use, or transformed into LaTeX for publication), it's a matter of writing a fairly simple converter, rather than trying to scrape the site or do other PITA stuff.