Yes, it's always possible that something can go wrong during an install or repair install. Anytime you make major changes to a system it's best to make a backup of your system. Of course a backup only works well when it's restored to the same system, otherwise you are back to the same situation you are in now.
Windows also has a file and settings transfer wizard, but I'v never used it so can't explain how to do it. I can post a link to it though.http://support.microsoft.com/kb/293118