I got a hold of the admin for ffxi-atlas.com. She was having some trouble on server admin side of things. I offered to help and she accepted. The server had some intrusion problems in the past so I did a few things to clean/detect any nefarious code/applications. There was also server misconfigurations that caused problems while trying to do routine maintenance to the sever.
I can't guarantee that it is 100% free of malicious code but I think it's much better off. If you notice any security related issues, you can report them to me.
Some things I did:
Scanned for rootkits.
Scanned for suspect php files.
Scanned for suspect iframes, found a few and removed.
Installed a security module for php.
Black listed some of php's infamous functions.
System-wide update.
PHP update.
Installed a different webserver.
Set up firewall rules. (nothing was set before)
BTW some pages might not work either because of depreciated php api or lack of or broken http rewrite rules.