Backed Up Music/Missing Music/Ipod File Transfer

Hi there!
I recently rebooted my computer (Windows XP) back to factory settings, which obliterated my iTunes. I had backed up my files (or so I thought) by saving my "iTunes" folder from the "My Music" folder onto an external hard drive--as suggested by the New York Times tech section. When I rebooted, reinstalled my iTunes start up disk from 2005, and transferred my music back into the correct folder, very few songs seemed to have survived the transfer--including none of my purchases and none of my playlists.
When I then updated iTunes to the current version, all my playlists and my entire library came back, but often in name only. Many, many songs--including many purchases--now have little exclamation points next to them that indicate that iTunes cannot find the original file, yet they are listed, thus taunting me that iTunes knows I own them, but refuses to cooperate. This is true both when the external drive is plugged in and when it's not. In addition, the blocks of songs that made it versus those that didn't seems very random--it's a mix of downloads from early on, recent trips to the iTunes store, and in between.
I know that it is my responsibility to back up my music, but I thought I had taken appropriate precautions. I have read in a few other postings about the option to select File-->Transfer Purchases from Ipod (all of my purchased music is alive and well on the ipod), but nothing really seems to happen when I do this. How do I know if it's working? Is there a trick to using this tool? Having tried it, I have seen no removal of the exclamation points, and I'm worried to do it wrong in case iTunes erases my ipod as well.
Any pointers or assistance would be very greatly appreciated!

hmmm... ok, so iTunes has updated itself to version 8.2 something since i first reinstalled the 2005 version, so i think it's entirely current. i am happy to remove this version of itunes and start over without reinstalling the 2005 version, if you think that will help. i'm just not sure exactly how to go about doing that. i'm also not sure how to get around this full disk warning, as it also happens when i add the library to the desktop rather than try to work from the external HD (which, it seems to me, should give it the full use of my internal hard drive to operate, which is far from full).
so, let's say that uninstalling and restarting iTunes won't save me or my music. how do i then go about returning the music to itunes from my ipod? i'm so sorry for the peppering of questions, i really am a technologically lost cause...
to clarify:
1. should i uninstall my iTunes and start over?
2. if yes, how do i do this without the 2005 start up disk?
3. if i do this and my music doesn't seem to automatically recover, should i then try the shift option?
4. how do i get around the "full disk" warning message if it continues to happen?
5. if everything else recovery-based fails, how do i transfer my purchased files from my ipod to my itunes if nothing seems to happen when i try file-->transfer from ipod?
thank you both so, so much!

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