Secondly, I can't get past the homepage because of some weirdness with the links that are being made. ex:
<a href="//admin/">Course Administration</a>
My browser (FF3) is parsing that to mean http://admin/ which doesn't work.
I suspect it has something to do with Webwork expecting its config files to not have trailing slashes, changing $webwork_url to just a slash means that WW is doubling up on its slashes which is throwing off the relative/absolute logic in my browser.