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By any chance had you recently upgraded your ITunes to ITunes version 9 or higher? Tune Tools used to work fine for my Ipod Classic 80 gig, but as soon as I upgraded my ITunes to version 9, the Tune Tools 2 stopped working, and I got that exact same java.lang.exception error.
If you have updated to ITunes 9, there isn't anything you can do about it.
I remembered that I had to reset my ipod once before and since I had already uninstalled and reinstalled itunes I thought it must be the ipod. So, I pushed the enter and the play buttons at the same time for about 5 seconds to reset the ipod and when I connected it to itunes this time, it was working!!!
I know another way you could try formatting which may fix this problem. Restoreing just restores all the setting to your iPod yes it shoudl format as well but it may not due to an error or something.
To do try it another way follow these steps, first click on "Start" - "My Computer" look for you iPod when it's connect usually called "Removable Disk" once you've found it "Right-click" on it then click on "Format", once format is complete disconnect, then connect it again then run "Update" for your iPod and for iTunes, once you've done that have another attempt.
Good luck. Hope my solution was helpful in some way. Further problems leave a comment and i will get back to you.
Try checking for ipod for any corrupted files. If you use P2P software to "pirate" music, try deleting those files. Also try a different usb port, and if you are using a hub, plug directly into the computer.....which Mac do you have btw?