MacPro 2008 remote reconfiguration

Hi,
I am trying to reconfigure the drives on a MacPro 2008 remotely via Screen Sharing. The remote machine had 4 drives configured in RAID 0 (I know). I copied the contents of the drives (66 GB or so) to an external USB drive via SuperDuper and booted from the USB drive ok. Using disk utility, I set up one drive to be the OS/Apps drive, 1 for Time Machine and 2 as RAID 1. So far, so good. I then partitioned and formatted the OS drive. I used SuperDuper to copy the external USB drive back to the OS/Apps drive. I set that drive as the startup drive in System Preferences/Startup Drive and rebooted. After a long time, say 10 minutes or so, the system came back online but was booted off the USB drive.
I verified the drive and permissions in Disk Utility. Still no luck.
I repeated this process 2 more times with the same result. I am at wits end on this and would appreciate any thoughts.
TIA.

One more input:
I have iPartition and compared what it reported on the remote machine to my machine. Everything looks ok. Both report bootable (reserve 128M). However, my machine has another entry: MBR Type Code: HFS (Mac OS/MAC OS Extended) while the remote machine has no entry. Could this be a clue?

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Hello TheAnt,
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How To Install and Remove Memory Mac Pro
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MacPro 2008 remote reconfiguration

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