How do I fix broken song files in iTunes with songs transferred from my iPod to my computer?

Recently got a new computer but when I tried to transfer the files in My Music>iTunes to my new computer I realized that only about half the songs in my library have folders in the iTunes folder, even purchased songs (no idea why). I could download mp3s of every broken song and re-do it that way, but I would rather figure out a way to restore the files from my iPod and save a lot of time.
I enabled disk use on my iPod and dragged the folders from iPod_control>Music to a folder on my desktop but the songs are all assigned random four letter names. I don't know if iTunes will be able to detect the right file to restore each song if I just direct it to this folder (using the prompt when you try to play the song), not to mention that the random songs are broken up into 49 separate folders so I would just have to randomly guess which folder to direct it to (I have 1993 songs). If I drag all the files into iTunes will it just create doubles of each song? I don't care about play counts, I don't know if that's stored in the song file, but it's not a big deal for me to replace all the songs in iTunes with the files from my iPod as long as all the files work.

Thank you so much! I now know how to convert AIFF audio files to ACC files, and I can keep the original AIFF file! One other concern though -- how do I tell which is the bigger AIFF file and which is the new smaller ACC file? iTunes doesn't have an obvious place/window that tells me the audio file size. Is there a way to tell the two apart. It looks like it creates an identical file name, not even a "copy" extension or anything -- so it's impossible to tell them apart. Is there another secret here?
g-5 Mac OS X (10.4.8) iPod Nano

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Thank you so much! I now know how to convert AIFF audio files to ACC files, and I can keep the original AIFF file! One other concern though -- how do I tell which is the bigger AIFF file and which is the new smaller ACC file? iTunes doesn't have an obvious place/window that tells me the audio file size. Is there a way to tell the two apart. It looks like it creates an identical file name, not even a "copy" extension or anything -- so it's impossible to tell them apart. Is there another secret here?
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PodUtil Mac and Windows Versions
iPodCopy Mac and Windows Versions
PodPlayer Windows Only
iGadget Windows Only
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How do I fix broken song files in iTunes with songs transferred from my iPod to my computer?

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