How can I fix my iTunes Media Layout?

I've been using iTunes for several years, and all the time I've let iTunes manage my library layout.
I outgrew my primary disk a long time ago so I have my iTunes Media folder location on an external drive, but I have both 'Keep iTunes Media folder organized" and "Copy files to iTunes Media folder when adding to library". In addition, I will occarionally run "Library -> Organize Library" just for fun.
Recently, though, iTunes has been putting my media files in strange locations. Really, really strange locations ... like ...
/Media/Movies/<* name of random music album *>/<* name of random movie *>
or
/Media/TV Shows/<* name of random movie *>/<* name of random TV show *>
Now I'm noticing that it is getting worse, and now I'm starting to find that files are missing or corrupt. So far, my backups have saved me, but I've stopped buying from iTunes because I'm worried that I might end up losing media that I buy from iTunes before I get a chance to back it up.
I've checked my disk drive and there is no filesystem corruption.
What the heck is going wrong? and How do I fix it?
~ thornton

I just tried the instructions here:
https://discussions.apple.com/thread/4882558
And I lost all my media and preferences.
iTunes now only sees my iTunes purchases, and they all have "cloud" icons (meaning they are in ICloud and not on my local disk).
All the movies and songs and books that I added from other sources are gone.

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