If you used windows disk check, nothing you can do about the bad sectors. If you used disk check, windows will mark those sectors as bad, try to move the data to another sector (if possible), then never use that sector again.
Cleanup your hard drive w/ disk cleanup and disk defrag. Kind of a vague statement, how much are you missing? Could be the bad sectors if it is a large chunk. Could be your computer was placed in hibernation and hasn't deleted those temp files that it loads to the hard drive.
Cleanup the drive w/ the above information and restart - see if that helps.