You need to find out how the pisher got access to your server. ssh? broken php application (and abused the apache user)? Any other ports open (like webmin ports)
Still any open port as a backdoor open to the pisher? I got hacked once because of a faulty PHP app, and the hacker installed some backdoor listening on an obscure port.
Start looking at /var/log and scan all log files. Try to identify something unusual.
to see if any strange program is running. And you might consider installing 'chkrootkit' and run a test. Also do
and see if something strange on an unusual port is listening. HTH