The FTP server is restored and somewhat better secured.
I do not know what exploit they used because all of the known exploits for wu-ftpd I had fixed, so this is one not known, however, it would appear they only had anonymous user permissions as nothing outside of the ftp directory was disturbed. Since the server mounts the ftp directory off of another file server via NFS, I have chattr +i the files and directories they should not be allowed to change on the host machine. Since chattr does not work across NFS there is no way for them to change it even if they were to somehow get root access so this should largely secure the server. I am going to create a apparmor profile for it just as an additional security measure.