I think I have some or most of my issues figured out. First, the system was unstabel with Crossfire enabled, so I disabled that. Then I noticed that my video performance was laggy with one card running three monitors, so I disabled the Eyefinity group. Then I lost one of the mini-DP to DVI adapters, so I had to swap that out with a spare (maybe I can RMA it). After that, I went to shutdown the PC, and the rig would not completely shut down. I went through a couple days trying to figure that out, at which point I think it may have been related to either the AMD beta driver, .NET 4 or the Asus Rapid charger. I installed the new beta 11's last night, took off the Asus rapid charger, and it seems to be better.
The only issue I have left is a boot error on one of the SSD's in the raid 0 array, but the system is working fine ATM, and I can reset the error through Intel RST.