Hmm, don't just focus on the server, and don't do anything drastic to
alert
that you're onto him/her!
Goto your permeter devices and turn on logging like mad
(routers/firewall)
so you can codify events (assuming that he/she is coming from the
outside).
Also, on the inside, pop in a sniffer on that subnet and capture
everything
- if you can't read the traffic at least you can start homing-in on where
it's originating, and that might divulge what programs/services are been
hacked... START A CHAIN-of events!!!! Document everything you notice and
what you do/did but try not to change the system - if it goes to court
you'll need it. Wish I could offer more but I'm not a unix/linux expert
(yet). Please keep us informed to let us know the progress.