If you decide to do a clean install on any of the drives make sure you only have one drive installed when you install the OS. Having more than one drive in place when you install can be problematic if you remove the second (storage) drive.
@kenrivers - I'll take that into consideration this time. I managed to fix the problem by going into the Windows 7 setup and clicked on "repair your computer" and I was almost immediately prompted with "Start up problems detected on hard drives. Do you want to fix" or something along those lines. And so now the problem is fixed. I also wiped the OS on the SSD to start from square one again so that I don't run into the same problem twice.