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Z77A-GD65, "Missing Operating System" after running Live Update

Update:10-11Source: network consolidation
So here's the brand new computer I assembled:
$309.99 HIS IceQ Boost Clock H795QC3G2M Radeon HD 7950 3GB 384-bit GDDR5 PCI Express 3.0 x16
$219.99 Intel Core i5-3570K Ivy Bridge 3.4GHz (3.8GHz Turbo) LGA 1155 77W Quad-Core Processor Intel HD Graphics 4000
$199.99 Acer G276HLDbd Black 27" 6ms (GTG) Widescreen LED Monitor
$179.99 Western Digital WD Black WD2002FAEX 2TB 7200 RPM SATA 6.0Gb/s 3.5" Internal Hard Drive
$159.99 AZZA Hurricane 2000 CSAZ-2000 Black SECC Japanese Steel ATX Full Tower Case
$154.99 Intel 335 Series 2.5" 240GB SATA III MLC Internal Solid State Drive (SSD)
$154.99 Intel 335 Series 2.5" 240GB SATA III MLC Internal Solid State Drive (SSD)
$144.99 MSI Z77A-GD65 LGA 1155 Intel Z77 Motherboard with UEFI BIOS
$119.99 OCZ ZT Series 750W Fully-Modular 80PLUS Bronze Power Supply
$99.99 Kingston HyperX Beast 16GB (4 x 4GB) 240-Pin DDR3 2400 (PC3 19200) RAM
$99.99 Logitech G930 USB Connector Circumaural Wireless Gaming Headset
$99.99 Microsoft Windows 7 Home Premium SP1 64-bit - OEM
$74.99 ASUS Black Blu-ray Burner SATA BW-12B1ST/BLK/G/AS
$59.40 CNPS9900MAXR Red CPU Cooler
$34.99 2 yr Replacement W/ ADH plan For (Acer 27" LCD)
$10.99 LITE-ON SK-2030/B Black PS/2 Wired Slim Keyboard
$9.99 LITE-ON SK-2035/B Black USB Wired Slim Keyboard
I wanted to have the SSDs in RAID0 with Win7 and the games on it, then a volume on the 2TB that the RAID backs up to, with the remaining 1.5TB just free storage space in another volume.  I couldn't get raid past Win7's Where Do You Want To Install screen during installation, so I ended up installing the OS on just one SSD.  I figured I'd backup the functioning OS to the 2TB then rebuild the RAID array and copy the OS back onto it.
The system had been up an running for a full day, being updated left and right nonstop, several big games put in, etc etc, everything was running fine until I decided to run MSI Live Update and started pumping in updates.  Constant errors as I went along, but generally it'd just skip to the next installation attempt.  When it got down to updating the BIOS and did it's DOS injection thing, it for forcefully shut down the PC, restarted, did Post, flashed the BIOS wallpaper, restarted again, Posted, no BIOS wallpaper, just endless "Missing Operating System".  Walked away, went to bed, back up and at it for a few minutes (Will be back tonight for however long it takes to get it fixed).  I switched the BIOS switch over, no dice.  Feels like it's a BIOS "OS" that's gone, and that a BIOS reset/flash is in order or something, but I've never done these things.
Thanks in advance for any rendered assistance that leads to resolution.

The Best Answer

The SSDs are definitely hooked up where they're supposed to go; the motherboard had a little sticker n' everything for where the two SSD dedicated SATA 6.0gbps ports were :P  AND my case has 2 specific slots for SSDs which don't use the hotswap electronics PCB passthrough like the other 4 bays, which is where the 2T is installed.  I was going to take the 2TB out and hook it up normally and see if that changed the speeds, but I'm leaning towards wishful thinking.  Did I mention I went and made several volumes with different file cluster sizes to test and see if that was the issue?  Alas, all were borked.  It still confuses me though because every once n' awhile it'd do massive burst speeds the way it's supposed to.
As far as I can recall I'm using up to date BIOS, the last one or two.  One BIOS switch is set for the last BIOS, the other switch is a step back devoid of the Windows 8 stuff.  I believe I have all the drivers up to date as well.  Intel 335's are literally brand new, mine hadn't been more than 3 weeks old off the production line when I received them; IE, they should pretty much have the latest firmware on them which spares me the risk of destroying something precious 
I MIGHT have a SATA external enclosure around here somewhere, if so, the 2TB could go in that for additional testing until I figure out where it's sustaining speeds of 2-10MB vs 100-150MB/second.
Meanwhile, the good news is that the system has been fully operational and hella stable.  I hadn't slept in almost 3 days, playing and installing stuff nonstop.  The system continues to run cooler ([email protected] CPU speed) as the thermal paste sets in, the knocking sound of the fan in the PSU has gone away upon me reawakening a bit ago, and amazingly, this massive system (with EIGHT fans) draws only 60-65 watts while desktopping.  That's just astounding