I've been working over the last few weeks making tweeks on improving the site load speed with varied success.
The good news is that we've located the source of the slowdowns on our site, the bad news is that it appears to be a form of PHP injection attack. We'll be working to identify the source code that's causing this for the next few days.
For now, comments, login, and registration have been disabled and other features will be taken down one by one for analysis.
UPDATE: The bulk of the script was removed successfully, security features have been added to prevent future injections. Site features will return shortly in the next few days.