Unable to get Command Center to work, Main I/O USB issues

Hello everyone! I'm new to the Club and I come to you looking for help. Here's the senario:

(EDIT: Aurora is the system I purchased)

I purchased in Dec 2009, my system has been running great!

Until I decided to see what updates were available. I checked my BIOS and found I was running A03. Went online and found that the BIOS was at A11. So I ran the update and everything appeared to be ok. I restarted, and that is when my troubles began. My system would not POST, and nothing I did would get it started up. I could not access F2 or F12, it just hung there.

I contacted Chris and he assisted me in getting a replacement MB. I got it in yesterday and spent the evening, carefully pulling out the old and putting in the new MB.

I ran into additional issues when for I started getting a  blue screens or crashes every time windows started up. I was able to narrow that issue down to a bad stick of ram. (wether it went bad during or after the original bios update, i don't know). 

Once I got Windows running (on two GB less ram :( ). I got slapped with another issue, for some reason I had an Unknown USB Device, and my AlienFX (all lights) and Thermal Controller (not reporting any temp or fan speeds) are not working.

I contacted Chris again and he ran me through several things. Including:

*restting the jumper on the Main I/O

*reseating all cables

*attempting to run a diagnostic which resulted in this error: 5D00:0009 - UUTUSBTM- DEVICE_INITIALIZATION_FAILURE user must reattach unit on ROOT HUB port 1 and re-start test.  The Main I/O was not in the available items to test.

On my own, I tried moving the Main I/O USB cable to the other MB ports (USB2 and USB3) with the same results. I know all the ports are working because the HUB on top of the system is working fine for each of the inputs.

I also disconnected the USB from the Main I/O and turned the unit on, and some of my lights turned on (alien and bottom front panel) and they were white. but as soon as I plugged it back in these lights went off.

Does anyone have anything else I can possibly try? (I stumped Chris on this one and he suggested I reach out to you guys).

Thanks for your help!

Wil