Our server was taken over by a hacker through a long existing hole in our web security that was discovered recently. We started out adding some new hardware and software last wednesday to plug the hole. When "she/he/it" (say it fast and that's how we feel!!) discovered our intentions, they took down the server.
Since then we have been working to rebuild the box back to a more robust and secure machine. Today we finally finished! It was touch and go there for a while too.
While no system is impenetrable we now have a professional installation that will guard us against most attacks. You will probably notice a performance improvement as well.