Update time!
I have now taken this machine through several rounds of trial and error diagnostics to try and Isolate the problem.
First I ran Memtest 86+ v4.2 for about 36 hours. 11 passes with no errors.
Next I disconnected the the Back Plane and used a new SATA cable and a 500GB WD Black (new) i had sitting around and did a simple install onto this drive. BIOS was set to AHCI (no RAID) for the drives. This worked great, no errors.
Next I put the same drive into the Front Trays and plugged in only bay 0 on the Back Plane and did the same install as above. no errors.
Next I Put one of the 2TB WD Se drives into the same bay and repeated the above. No errors.
Next I plugged in Bay 1 and switched the BIOS to RAID. Setup a RAID 1 array and performed the above install. The main difference here was that I also needed to install the RAID drivers for the windows install, and install the RAID GUI into windows and initialize the Array. Took longer this time, due to the time taken to Initialize, but otherwise completed without errors.
Just now, Instead of proceeding to a RAID 5 setup like I had been doing before, I instead decided to experiment with a storage pool instead. I shut the machine down and plugged in the rest of the drive bays. Now there are x6 2TB WD Se drives in the machine. 0-1 are a RAID 1 set, the other 4 (2-5) are simple drives. It seemed to boot fine, however when I went into the file and storage manager in the Server manager software, and clicked on one of the drives shown, the system hung. The Mouse still moved, but nothing responded. And now Bay 5 is lit up!
So Now I need to wonder if this is a Drive error problem, a Back Plane issue, cable issue..... [*sigh*] ... more testing.....