If windows boots, do a repair install. This used to be really easy with XP because windows didn't have to boot. You could do it from a XP cd. That changed since Vista. Now you have to be able to boot into windows to do one. But it sounds like you can boot windows, so.....http://www.pcworld.com/article/243190/how_to_repair_a_corrupt_windows_7_installation.html
That's how you do it. And it preserves your programs and everything.