Don't know what troubleshooting you've done so far but have you tried just connecting either one of those drives directly instead of going through the raid controller? Then when you fire it back up, connect your PC to the serial port and watch the boot process.
I had a system do the same thing once and it did turn out to be the raid controller. Fried both drives! Neither one would boot the system directly and when I put in the new one connected to the raid controller it wouldn't boot either. Had to bypass it completely. I had to replace the whole raid system, drives and all.
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