Can you plug the Windows-formatted iPod into the Mac and simply grab the music from there? The Mac and the automatically-syncing Mac-formatted iPod should have the same library (or at least some identical playlists depending on how you sync the iPod).
Otherwise, we may need more information before we can get any further. Hopefully you have the rights to all this music because otherwise MacRumors won't be able to help you. 🙂