I'm going to try all these suggestions when i get home. Here are some more details in case someone thinks of something:
I had three drives:
OS drive, 300GB velociraptor
storage #1, 1TB, WD caviar black
backup #1, 1TB, WD caviar black
All of them are SATA, connected directly to the motherboard.
I removed the backup #1, and replaced with a 2TB Hitachi drive. Before I did that, I first copied the files over using the drive in an external esata enclosure.
Then I removed the cables off of backup #1 and connected to the new drive. now the computer gives the boot error. That's when I tried using the Repair install on the Windows boot disk. I chose the "startup repair" option. It overwrote the MBR a time or two. I also tried fixing the MBR using Liveboot 2012. Neither did anything.
I did come across some online advice saying to do something with my boot order. You guys mentioned that here as well. I'll try that tonight. i don't want to reinstall Win7 from scratch. I just did that last month.