Hello,
 
A bunch of the theming issues have now been fixed.
 
The problem came from the new MW software using a new PHP script (loader.php) to pull in the javascript and stylesheets instead of having the browser pull them in directly.  For security and aesthetic purposes, I have an Apache rewrite that redirects all but a specific list of PHP files.  Since loader.php is new, it was not on that list, and Apache wasn't letting it run.  Adding that file in the RewriteCond fixed it right up.
 
The good news is that we can now take advantage of centralized loading of css and javascript.  Since the majority of page loading time comes from dozens of HTTP requests for these resources, these front end optimizations should make the wikis *much* faster.
 
I don't know if that fixed the red link issue offhand, since I can't find any pages that have broken links.  Anyone who knows of a page I can test?
 
-Matt