As you probably noticed, the site was not accessible for ~2 days. The reason was not related to the earlier malicious data wipe, nor the following webserver upgrade issues.
In this particular case, two identical drives bought the same day decided to start failing on the same day, causing the system to die a slow and agonizing death. That prompted the purchase of four new drives, as well as bringing the machine itself home for a thorough checkup.
Things should be running okay now, the only issue I found so far was arcomage's main.php being truncated halfway - which was very easy to repair.
Again, thanks for sticking around.