Here is what I have found:
Both HDDs appear to be alive and well. No errors on them. I used something called smartctl to check the drive status. Every other utility I spun through has echoed the same. I can also see all the data on these drives if I use a connection other than internal sata. When I hooked up the drives in an external usb or external sata I could see and read all data. These drives were not hooked up in an array of any sort as a side note. A memory check showed that there were no issues there either.
So long story short, this is looking more and more like a hardware issue. The thing that I can't figure out though is why I would be able t see the drive on my post screen but then be unable to access it when I'm in any sort of operating system.
I don't currently have any spare drives sitting around other than an old IDE. That really wouldn't help my in diagnosing this issue however. I could however probably leverage it to be the main drive for a short time as I get things sorted out, using the other drives externally, but I've already ordered a couple new drives to set up in an array. Looks like I might be throwing a new motherboard on that list as well.
I did notice that newegg had a lot of ill reviews for this MB due to quality and then RMA (which I'm outside of the 30 days by a couple of months now anyway). Therefore I would recommend to stay away from this board, or at least think twice, if you were considering.
thanks again guys for your great suggestions.