Under the bonus tools I ran the "duplicate File Finder" which took over 5 hours and came up with 3027 duplicate files. How in the world could any one know which files to delete?  

Be careful not to touch any duplicates in the Windows folder. Generally if the files are truely identical I would delete the older versions. However the file locations are important. The safest but most painful way to do this is to change the last letter of the file extension to a  different letter (keeping this letter constant).  This way you can reboot and re test the software associated with the duplicate file.  If the software malfunctions, go back and correct the specific extension.  If the software works fine you can then locate and delete the duplicates.  Generally this is not worth the hassle particularly since even 3000 plus duplicate files don't take up too much space.
I might be too cautious and Ray might have a better solution.

   I added the duplicate file finder because a user had asked for it.
   If I used it, I would mainly use it to remind me of times when I had installed the same program to two different places or something like that.  These should be obvious.  You should always be cautious about removing duplicate files.