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Also this should prompt you to make your server more secure. Try browsing these forums with lots of good information. You might want to disconnect it for now to be safe until you know it is safe to bring back up on the net.
Next to the fact they might be using intermediate servers they might have zapped shell and login history as well. Chkrootkit can find zap AFAIK, but can't find deleted data. If you really want to know what traces they left after they shredded stuff you'll have to dd an image of the disks, partitions and run TCT.
Mind you, it ain't a trivial task so I'd only recommend it for situations where it is crucial to have the knowledge, it'll take lots of time and you have to know how to construct the timeline and interprete the pieces to build the puzzle. Also chances of reconstructing get slimmer the longer the system remains active (disk writes).
Btw, would you mind posting your general network layout (if any), what daemons you where running, if you where up2date and if you got *anything* out of *any* logfiles?