I had a similar experience as the OP years ago. Luckily, the attacker forgot to erase a bash history so I could recover almost all the command lines. It seems t

I had a similar experience as the OP years ago. Luckily, the attacker forgot to erase a bash history so I could recover almost all the command lines. It seems that most of these operations were pretty standardized; they first downloaded a bunch of exploits from another cracked site, then in my case they tried to run a local exploit to gain a hole in kernel (it was a Linux 2.4 box whose privilege escalation bug was fixed just weeks ago). I had a patch applied to the kernel so it didn't succeed. Then they started an IRC bot as a disguised name (like /usr/X11/X or something) and left. I felt embarrassed but in hindsight it was a pretty good lesson.