Converting MPEG-4 Audio Files back to iTunes

So my computer crashed from Vista's Service Pack 1. The cause of the crash was unknown at the time and I thought I had a virus so instead of backing up files which could contain virus's. I just reformatted my computer.
Now I have about 10 gigs of legal music from various place (CD's, iTunes, Friends) which are all already on my iPod. I know there are 3rd party programs to retrieve these songs, but I know a little bit about computers so I just did it myself.
The problem I am having is converting the MPEG-4(m4a) files so iTunes recognizes that these are music files like a MPEG-3(mp3). For some reason the actual CD's I bought when burned saved under both file types, I have no idea why. So basically I am missing about 1/3 of my library.
Any help on how to get these files back onto iTunes from my iPod without re-burning 100's of CD's?

Some of those solutions are free. You can also take a look at this user tip:
http://discussions.apple.com/thread.jspa?messageID=613166&#613166
The solution presented is free albeit a bit involved.

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