If the connections on the headunit look okay, the next step would be to do a voltage check on the pinouts for the rear & sub. I could see the one side going bad in the rear. Maybe even both the rear channels. But I can't imagine that the head unit would have the rear channels and sub channel fried. If you get voltage from the head unit outputs, then check the voltage on the amp outputs. If all of that fails, then I'm at a loss. I would think it would be a straight run from the amp to each speaker, but there may be some other connector involved somewhere inbetween.