This is why I have always advised keeping two separate drives or partitions - the system drive for operating system and installed applications and a drive for all user data. That way you can reinstall windows without risking loss of data files buried in all those interminable "My this" and "My that" folders. If you have to run a full reinstall then I would copy the whole of the contents of your username folder from the system drive plus any other user data files you are aware of onto an external drive then run a full format and reinstall.
There might be two things you could try to get your system working. Running a chkdsk and System file check, never hurt. To run the System File Check, open an Administrative command prompt and type SFC /scannow. Maybe it will replace some files that have been damaged or corrupted.
Chkdsk might help clear up any drive corruption, if that is involved.
But if you have Windows 7 SP1, you can download a like version from online and then do an inplace upgrade which refreshes your system and leaves your personal files in tack. Of course not 100% reliable, so back up first.