ITunes and I seem to have created duplicate files. How do I clean this up?

Question

Hello experts.  I have a conundrum I'm too inexperienced to reason out.  Hoping to tap your creativity.
I have a huge iTunes library I've created over the years.  50,000+ songs.  No problem, other than my desire to whittle through it slowly and pare it down to only the 22,000 or so I want to keep as my primary library.  I haven't gone through the effort of creating multiple libraries yet, I simply delete songs or albums from the library as time permits without deleting the original file.  I figure iTunes' database will be my primary and in the long-game, I'll create a new library that holds everything, but for now I'll just keep whittling the dB structure away until I get what I want (this is a slow, multi-year project I'm undertaking -- no rush here).
Here's my problem:
Most of these songs are physically saved in the iTunes folder on an external hard drive.  Some of the songs I added to my library from the iTunes store when the external hard drive wasn't connected to the Mac - so they are on the Mac's hard drive under the standard iTunes folder structure.  I have the "Keep iTunes Media folder organized" and "Copy files to iTunes Media folder when adding to library" checkboxes checked.
As I said, I've deleted songs from the iTunes app, but told it to "Keep Files" so that I could listen to them in the future if I decide to re-add them.  Yesterday, I ran out of space on the startup drive of my mac, so naturally, I figured I could consolidate any files on my hard drive over to my external hard drive and delte them from the mac. 
In iTunes, I went to File -> Library -> Organize Library.  I checked both boxes for "Consolidate files" and "Reorganize files in the folder..."  I let this run overnight to consolidate my library into one place.  Today, I found that the function was unable to complete due to lack of disk space on my external hard drive.  When I went to check the external hard drive, I found that iTunes had duplicated all of the songs that were on the external hard drive in their existing folders. 
For example, now I have a file under the structure:  iTunes library -> Music -> Blue Oyster Cult -> Heaven Forbid -> Cold Grey Light of Dawn.mp3
And I also have a file under the structure: iTunes library -> Music -> Blue Oyster Cult -> Heaven Forbid -> Cold Grey Light of Dawn 1.mp3
So now the immediate problem...  The consolidation didn't finish, so I don't know exactly how much duplication iTunes created.  I checked my library, and sure enough, the song in the library is pointed at the duplicate file (the one with a 1 at the end).  I don't have the option to just copy the iTunes library to another external drive temporarily (or not easily, at least).  I checked out a bunch of duplicate file cleanup programs, but the ones I found (and I even purchased Gemini's dupe file finder/cleanser) don't seem to inherently choose the correct duplicate file that is linked to iTunes library dB.  I can't realistically pick and choose from the thousands of files that have been duplicated.
I decided to change the advanced preferences in iTunes to an entirely new folder on the External hard drive.  Then I could just go back into File -> Library -> Organize library and select only the "Reorganize files..." checkbox without selecting the "Consolidate files" checkbox.  I figured this would just move all the files that are in the iTunes dB to the new iTunes folder.  Ummm.... but no.  Apparently this "Reorganize files" checkbox is only available if you select "Consolidate files"...?   To be clear, "Reorganize files" is greyed out.
So to summarize:
1.  Why did iTunes create copies of existing files in the exact same location they were in?
2.  What is the right (and I pray easy) way to get my library back to the right size and consolidated into one place?   I'm still dangerously low on disk space on the mac...
<sigh>
Thanks for reading through all this! 
Tim
Mac Mini  OSX 10.8.3; iTunes 11.0.2 (26)

Answer 1

See this thread for background on why iTunes can end up with duplicates and how they can be systematically removed. The script there is for Windows users and the "show duplicates" menus have moved around in iTunes 11,  but the advice on clearing recently made duplicates should still hold.
As given in my older post "Reorganize library" is meant as a one time command to change the structure of a pre-iTunes 9 library into the newer layout that places music in its own subfolder of the media folder. Once used, if the option becomes available again that suggests that a file called .iTunes Preferences.plist in the media folder has been deleted or editied.
See also this post.
tt2