(!) How to locate the original file for missing songs?

song could not be used because original file could not be found. Would you like to locate?
I got this message when I last tried to synch my ipod.  The message said there were 100 files which could not be found.   Actually more than 100 songs show the exclamation mark that says the file can not be found. 
Previous posts on this issue suggest the underlying file has been changed or moved out from the ITunes organisation.  Well the last time I synched my ipod on Lion a few days ago it was fine.  On Sunday I wiped my hard drive, carried out the upgrade to Mountain Lion as a clean install, and used Migration Assistant to bring my user data over.  After that I ran cclean and disk utility permissions and disk verification.  Then this happened.
I migrated my  iTunes Library to an external hard drive six months ago. That was disconnected during the upgrade so I am not sure why the files can’t be found now.    Anyway, I want to recover the missing files .  I could not find them by name, album or artist on the external drive.  So I thought I would find them in Time Machine backup #1.  I couldn’t!.  Nor could I find missing songs on my alternate Time Machine backup #2.  Both Time Machine backups are set to include the external drive.  Songs recognised in iTunes are visible in the backups, but not the ones that are missing.
I have a third backup volume which was a clone of the Lion setup before I did the upgrade, but I can’t access this or Mac for a few days.
I did have some permissions failures after the 10.7.4 upgrade which resulted in creating 2 new standard user accounts.  Maybe I’v e got some files across these users?  But in that case I’d have seen problems before the upgrade?   I notice a fair number of these are compilations imported from CD about 4 years ago.  Bu tnot all. 
(1).  Is there a smart way to list all the files that are missing?
I can scroll through all of  ITunes Music to see where there are exclamation marks.  I’d like to only list these missing songs.
(2).  How can I locate the missing media files?
-  a search on Name / Album / Artist hasn’t found them in live drives or on TM backups.  I’ve still got the missing songs on my iPod, however.
Once I can answer these questions with your help I’ll know what would be the best way to try to recover, and to work out what went wrong.  I’m shocked that I can’t find them in backup.   Eventually I can restore audio from original source.  If they were photos that went missing from library and backups then I would have no way to get back!
(3) could this happen in iPhoto?  (shiver)

Thanks for taking the time to look at my problem.  Shared is empty and I didn't back it up - I only transferred the standard and Admin users to the clean install of Mountain Lion.
But I got some valuable insight into how the iTunes library is set up from your article on split Libraries. I'd like to see it in the Tips for iTunes for Mac.   My Itunes library was set up in pre-Itunes 8 structure, and as I'd moved it to an external drive it didn't get migrated to the new structure in recent upgrades, perhaps?
I found your article extremely useful : https://discussions.apple.com/docs/DOC-3991.  That gave me the means to restore the missing files more quickly than getting the original CDs out and re-importing them to iTunes.
So I've now restored the missing files and started the backups rolling ....
I still don't understand how they went missing.  However the best backup was the Ipod itself.

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