To answer my own question, I was able to get the windows recovery console open from the install CD and use CHKDSK C: /R and recover the corrupted information. Windows launched successfully after that.
I installed a new cooler in my machine last night, and had to reboot it several times due to a poorly seated video card. I am afraid I may have corrupted the windows progam because of the multiple shutdowns. I tried to do the installation repair, but the installation disc does not recognize that windows is installed on the hard drive. I do have my system backed up on a Western Digital external. If I reinstall windows, can I get my system back to where it was by restoring after a clean install?