Well I fixed the problem without pulling fuses.
1. unplug ipod
2. switch ipod manually to music
3. manually start playing a playlist via the ipod's interface
4. plug back in to the USB port while ipod was playing
5. switch back to USB from line in default when ipod was unplugged
result: sync started playing the playlist I had selected and stopped complaining about indexing.
However later it said "building voice commands" and wouldn't let me use voice commands.