(1) HTML cannot express all formatting which CSS can express.
(2) The output is now hardwired to mix content and presentation. I hope you're not throwing away the clean content files.

Can you accept style="..." in your HTML tags? Those are still CSS, but without the dependence on external style sheet files.

If you can accept that, you can probably just accept a <style>...</style> ahead of the body. That should be trivial to piece together. You just replace each stylesheet reference with a style tag.