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John, thank you for helping out here. It's greatly appreciated.
blackdiamond, when you said you've had downtime for hours at a time, that only leads me to believe that the problem could be with an account on your server running an intensive looped process at certain times. We have these own issues on our shared servers.. accounts cannot be allowed to run any type of scripts they want due to this fact.
If you go into WHM and click on CPU/Memory/SQL Usage under Server Status, if any file path is in red or yellow, that user definitely needs to look into their resource usage. If you don't see anything suspicious at all recorded there, then the problem will take longer to narrow down.
As John said, please post your ticket number here and I will look into the responses so far on it and have a look at your server.
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