New Mobo Install - Stuck on "loading operating system"

I just upgraded to a gigabyte 990fxa-ud3, with a phenom 1100. I began the process to try and upgrade the bios which also was a failure due to the inability to recognize my flash drive. Comes up as drive A under Qflash, but doesnt recognize the files on it. It has been formated correctly, so i dont know there.
But while doing this, i noticed that my main hard drive, with my windows install, wasnt being recognized by the bios. So i tested it in another computer and is readable, so im assuming that it not showing up isnt a failed hard drive. My second hard drive is recognized, but using the same cables, it still cannot find my primary drive....

Im at a loss of options right now, i can only think of copying my windows files from the primary hard drive, to the secondary drive, which is currently pretty full, and hoping for the best as far as trying to recognize the other drive once everything is bootable.

Any ideas or info would be appreciated. Thanks!
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  1. Also wanted to add that ive tried switchin the sata controller to both raid and ide, and still couldnt find said drive.
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