Thanks for sending me your FTP and AP Admin credentials. I first restored all the infected files that my plugin cleaned to see if that would fix your site but that was not the problem and your site still did not come up. Then, while looming for the cause, I noticed that the permissions on all the files in your html directory were 555, this did not seem right. So, I wrote a script to change all the file permissions to 644 and all the directory permissions to 755. That fixed it and once you updated the database credentials in the wp-config.php file your site was working again.
I have finished the Complete Scan once more and fixed all the infected files again. Nothing broke and the permissions are still all right. I’m not sure how the permission on every file got changed to 555, maybe you had something else going on around the same time, or somebody else was working on it too, any ideas?