Here is how I approached a similar problem.
For starters, I do it all inside of Media Center. Its super database engine can help you.
Note that my directory structure is:
[Artist]/[Album]/[Track #] [Name]
so that after I do a "Tools>Library Tools>Rename, Move & Copy Files>Rename (moves files if directory changes)"
(if a pop-up appears about duplicates, give it the OK to proceed.)
any duplicates have a (1) or (2), or ..., appended to the filename if there are duplicates or triplicates.
With that, I then create a smart playlist that selects upon a filename with a (1) or a (2), or... in it.
That playlist then contains all the duplicates, but it also may contain a random song that happens to have a (1) in the filename, so I double check it carefully.
After I am satisfied that the playlist contains only duplicates, I Ctrl-A to highlight all the files, and delete them. The pop-up gives me some options, and I select the recycle bin option, just in case.
You may need to adjust the above to fit your environment, but it should give you some manner of a starting point.