Dang, never thought of that! That's a great idea. So close to getting this working now. Only problem is that some of my pages aren't in the root directory so the CSS link doesn't work.
So close!
My first thought would be to make a symlink, but that's a kludge. My second though it is using str_replace on either $headinclude or $output, but I'm thinking there is a better way.
A quick search gave me this thread which led to this. Then, I saw a plugin at the bottom of the thread. Hope that helps some.