Hey, iTunes ain't that bad. On Mac. On Windows, it's a steaming pile of fail lol

I dunno, is it the bigger or smaller capacity iPod of that generation? Because the iPod file structure reads the firmware from a certain size partition, ie, 20GB or 40GB. You can't go 30GB. if you have the bigger capacity one, then just reflash an image of the HDD from the smaller capacity iPod, and install Linux on the remaining part of the drive.

Hope I helped, and good luck