Is there way via SSH (or WHM, if it has that functionality) to view specifically what files/scripts are causing the server CPU to be so high? For the past few days my server has been going offline a lot and all my server management will tell me is that there are processes taking up too much of the CPU, but in WHM I can only view CPU usage by account, not by specific file or process.
You can also run ps uaxww in order to see if there are any suspicious tasks (top command lists tasks sorted by resources usage, and not all tasks get listed)