After doing the chkdsk /R on my OS partition I was able to at least get it to detect the Windows 7 Element but still not luck with booting.
I switched my OS HDD to another SATA port (my Port 1, instead of 2) and then rebooted. Once I did that, Windows was again detected! I had to run through the system repair and then boot into Safe Mode and then finally do a system restore into an older working instance, but it finally works again!
So the key I guess was switching the HDD to another SATA, all my drives work too, so no damage!
Thanks for the help!