IPhone Restore relocated song files, Library all messed up!!!

Little history of my itunes library:
I recently got a new MBP and switched all of my music from my old G4 to the new MBP. (both machines had the save itunes version, so i just swapped the entire music folder, itunes playlist files, etc.)
Once on my MBP, I updated the library to iTunes Media Organization. Everything has been working fine, all music plays, seamlessly sync'ed with my iphone and ipods, etc. That is, until I recently restored my iPhone with my most recent back up.
After the restore, all of the music that was on my iPhone was moved out of the iTunes/iTunes Music/Music directory and put into iTunes/iTunes Music directory (as if iTunes Media Organization wasn't ever applied to those songs). Now iTunes can't locate those songs and i have to locate each song manually, which is something i don't want to do (23 gigs of music!).
The weird thing is that all the missing music files are still playable on my iPhone after the restore and after re-syncing.
Does anyone have any idea how to fix this problem?!?!
Can i revert my library back to the old itunes music organization?

BUMP

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