Update:
All the disks checked out fine with zero errors and I ran memtest for 6 hours without issue. I updated the BIOS on my motherboard (was quite old), reset all the settings to default, then disabled all the stuff I don't need (audio,serial, firewire, etc). I installed my LSI 3081E-R and I now have disks 1-4 on the MV8, disks 5-8 on the LSI and disk9, cache and parity on the on-board controller.
One thing that may have been an issue was I had the server on the carpet (not plush at all) with a bottom mount PSU, I noticed the exhaust air was "warm" so now it's on my desk.
So I'm going to do a parity check and hopefully if nothing bad happens I will be rebuilding disk 8 as I RMA'd because I didn't like the seek noise it made. I already have the advance ship disk from WD pre-cleared and I need to ship disk 8 back ASAP so I don't get charged $150.
Hopefully if I have another failure it will be limited to the MV8...
I'm also planning to rebuild either 3, 4 or 6 onto a new 3TD Red and then copy the data on the other two to other disks. They're 1.5TB seagates that I've had forever and are on multiple RMA... I think one is the original purchased drive. Actually disk 8 was just recently rebuilt from a 4th 1.5 seagate that was on it's 3rd re-certified replacement. I've just had enough with these awful drives.