O/S partition problem? GA-MA785GM-US2H

I recently upgraded my my motherboard, CPU, and ram and got things working just fine. On bootup, however, I kept getting the message, "SATA is found running at IDE MODE!" There was another message after it asking if I wanted to change it to AHCI mode or continue in IDE mode. It did this on every bootup, just like the manual said it would. I didn't know what it meant, so I just let it wait the 8 seconds until it moved on on its own. Well, that got old after a while, so I pressed "Y" to set it to AHCI mode. That was clearly the wrong choice.

After that, it would only go to the Safe Mode option screen. Every time I chose to start in the most recent bootable condition, or whatever that choice is, it just restarted and brought me to the same screen. I booted in safe mode, and then restarted, which brings me to my current problem.

It seems to be booting off the wrong partition on the hard drive. I don't really know what it's doing. When it boots now, I see the desktop that I had 2 years ago. It's now saying that major changes have taken place and I have to register Windows again. Well, I did that last week when it booted up properly on what I assume was the correct partition. It will boot far enough to tell me it's found new hardware and wants to help me with some drivers. Very shortly after, it restarts on it's own now.

I'm guessing I have to tell it to boot from somewhere else on the hard drive, but I don't know how. It restarts by itself when it goes into the "old" desktop. I'm very confused. Any ideas?

BTW: My 2nd drive that I use for storage is SATA. My OS drive is IDE. I unplugged the SATA while trying to figure the problem out so it's out of the loop.

I reset the CMOS, to no avail...