Best HD configuration MacPro
The Raptor drive as the system drive is very smart but I don't know if your system drive without apple's firmware will cause problem or not. In the past , it would be a problem but I don't know if that is still the case.
Set up 2 400G as the scratch disk and utilize the very last bay as the back up drive, that way you do enjoy the speed and provide some kind of protection.
However, why don't you get 2 external RAIDs and use disk utility to mirror it; that way, you will have a RAID 0+1 solution.
Meaning, you will have the RAID 0 speed and 100% data protection and no need to move the files manualy to your backup drive.
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