Restructure iTunes Library File Hierarchy While my iTunes library works, I have a lot of dead files and a messed up iTunes Music directory.

Right now I have a hierarchy that looks something like this

|-&amp;I
| `-&amp;I's Music
|   |-This Day Aria.mp3
|   `-Until the Sun.mp3
|-Archie
| `-Archie's Music
|   |-Heart Attach.mp3
|   |-Kingdom.mp3
|   `-Roll The Dice.mp3
`-iTunes Music
  |-&amp;I
  | `-&amp;I's Music
  |   |-This Day Aria.mp3
  |   `-Until the Sun.mp3
  `-Archie
    `-Archie's Music
      |-5upernova.mp3
      |-Heart Attack.mp3
      |-Kingdom.mp3
      |-Leto.mp3
      `-Roll the Dice.mp3


As shown above, many tracks are present in both iTunes Music/ and out, but not all. Only one is linked into the iTunes Library. Usually the one that's linked is the one outside iTunes Music/, but sometimes it's the other way around. Also not all tracks are duplicated.

I want to consolidate all the duplicated tracks into one, without unlinking tracks from iTunes, and flattening out the iTunes Music/ directory.

Anyone know how to do this.

The library is completely backed up. I also have an iPod that I can put the library on. If possible, it'd be great to pull the library off the iPod, which I'm sure is properly structured.
Have used Itunes for about 10 years now.   Keep you backups, but switch to the setting "Keep Itunes media folder organised" in the Settings.  At the same time I always check "Copy Files to Itunes Media folder when adding to Library".

Itunes sorts music per artist by default.   right clicking on any item can take you to the physical spot in you library.  Get over the apprehension and just edit the metadata.  

To get any music referenced by your library follow steps at http://support.apple.com/kb/ph1459.

After that all the your stuff should be in you ITunes library.