itune 11 folder structure mac 10.6.8

I had a hard disk problem, bad node, so I backed up all files and fixed the issue using the Disk Utility, then put everything back in place from a Time Machine backup. Everything is back working fine, however, my iTunes folders seem to have duplicated and multiplied. I now have a folder structure that looks like this:

user/music/iTunes/iTunes Media/Music

user/music/iTunes/iTunes/Music

There are music files spread across all levels; in music, music/iTunes, music/Itunes/Itunes/music, etc. with multiple duplicates. Plus multiple duplicate alias files.

There are also duplicates of itunes library files -- .itl and .xml.

When I open iTunes, it only shows a few titles that were bought through iTunes Store, but not all of them. Also my iphone apps are gone.

I have all of my music and apps up to date on my iPhone, but doon't want to sync because I understand that I will lose all those files in the process.

I was thinking of putting all the files into the user/music folder, opening iTunes and doing an Add to Library, but that won't fix the duplicates.

Any suggestions on how I gain regain control.