After Windows 7 repair, everything is gone...

 The first thing I did when I powered the system, I tried to update windows 7, failed twice. It just stuck on "Shutting down..." and didn't go anywhere from there. So, that ventually worked for somereason (3rd time is the charm I suppose.). Then I updated GPU drivers, installed antivirus, firefox, itunes, quicktime, uploaded 40gb worth of videos from my hd camera, pictures from my digital camera, began downloading an mmorpg, installed steam. Today, I restarted my computer, and for some reason it didnt want to restart because the sticky notes were open, it didn't have that problem before, I forced restarted it. Then it bagen repairing something, it restarted like 3 times, and kept on saying something about not deleteing anything. When I log in, nearly everything I installed and downloaded is gone! The only things that remained are the pictures and videos I imported from my cameras and the software that comes with Sony Handycam. But everything else like antivirus, quicktime, games, etc. is gone. The wierd thing is that when I check HHD for space, the space wasn't freed, like everything is still somewhere hidden. But when I go to like iTunes folder and check properties it says the folder is about 100mb large and there are almost 2000 files inside, but when I open it, there is hardly anything there and no itunes.exe. Anyone had the same issue? Also, if I use Custom Image disk DS provides, will it keep the overclocks?