My iTunes Library Is All Messed Up

I've tried to fix my library and everything got screwed up majorly and I'm not sure what to do. Somehow, my library is coming up in iTunes with the right ratings and such, but things have been moved around and I'm not sure what to do.
Basically what it looks like happened is everything was moved from my D:\Music\iTunes\iTunes_Music to the D:\Music\iTunes folder. But now although there are no duplicates showing in my iTunes, it looks as if tho there are duplicates on the hard drive when I look in the folder. And the worst part is, I don't think I can just go in and delete what was in the D:\Music\iTunes\iTunes_Music Folder because when I look in the folder, there are folders I see there that are not in the D:\Music\iTunes folder.
Any suggestions on how I can clean this up and keep the information from the library or am I screwed?

Do you have plenty of room on D: for another copy of all your music/podcasts/videos etc?
If so, I would go into itunes, and run the consolidate command. Use this article's directions. But make an entirely new folder named D:Media.
Tell iTunes to consolidate everything to D:Media.
Once it is finished and you verify that you can play your songs, videos, etc. you can delete the other 2 confusing folders.
Move itunes folder directions
http://support.apple.com/kb/HT1364

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