Keep in mind that re-encoding audio files already stored in a lossy format like MP4 will result in lower quality. You're essentially creating a "rip of a rip", and just like making copies of tapes back in the day, it degrades quality.
So don't get rid of those MP4's right away, if you have devices that will play them (and if you have iTunes, you probably do...) they will sound better than your second generation MP3 files.
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-Scott
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