ok, I thought by backing up my library from iTunes to an external drive I would have saved everything. I did a system reinstall with the manufacturer disks and when I connected my external drive, iTunes were no longer there nor Limewire. I have an iPod with all my files. How do I transfer the files over to iTunes without it being erased by iTunes.

When you do a reinstall everything gets wiped out. This means every program you installed like iTunes and Limwire is gone. Go and download iTunes again and then when you connect your iPod choose the option to not automatically add music/videos/pictures to your iPod.