I'd be very interested in any details of your approach that you could share. I added another comment to this thread with the details of what I've been working on for professional spec documents with markdown and rendering to PDF (testing with CSS now).
It's relatively low-tech, but it does work. First, I have some scripts to preprocess the Markdown and extract custom markup that I have built to do things that Pandoc's Markdown can't, but that I can still easily inline in the document. For instance, I replaced the source code markup with a custom one that generates LaTeX formatted the way I want it formatted. I use Pandoc to output LaTeX. I then have a series of shell scripts to postprocess this LaTeX to insert pre-rendered figures, re-introduce the custom markup as rendered LaTeX, or to massage the output so that the document is laid out the way I expect.
I'm planning to use this to write a book in the near future.
