>>jakels+(OP)
I am not an expert in incident reaction, but I thought the safe way was to image the affected machine, turn it off, take a clean machine, boot a clean OS image with the affected image mounted read only in a VM, and do the investigation like that ?
Assume that the malware has replaced system commands, possibly used a kernel vulnerability to lie to you to hide its presence, so do not do anything in the infected system directly ?