If you have a 40GB Hard Drive you are not going to see 40GB usable due to the fact that drives are marketed as being 40GB, but the actual usable space will be more like 37GB or 38GB usable due to numeric conversion.
It is possible for stuff to hide on your drive and eat up space if that is what you feel you have for a problem. To fix this you will want to search for hidden files and folders, but not all hidden file and folders are bad, so you will need to verify if its good or bad when you find them. Windows normally has hidden files and folders.
If the system slowed way down after a bad torrent, it could be viral. Have you performed a virus scan?