I would first get some sort of virus protection that you are comfortable with and run a full system scan. If your hard drive has bad sectors and you are running out of space I would recommend using Acronis and buying a bigger hard drive and moving the partition to the new drive and then expanding it inside windows. I would not touch the WinSXS folder or any folder for that matter inside the windows directory, it houses backup driver files and all rollback and uninstalls for each windows update.
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