Try repairing permissions first
If not then try restarting the computer and delete them before you open up anything

Have you done the hard reset on the iPod.

Plus it into an AC outlet (not the eMac) toggle the hold switch on and off and then hold the Play and Menu button until the Apple Logo appears....then...

instead of moving everything manually if you went into iTunes | Preferences | Advanced and selected your external drive as the storage space and then went to Advanced | Consolidate Library it would...

Unless your drive is having serious problems there is not much of a need for any of those....Disk Utility can take care of almost all of your problems