[mtelliott]

I concur with Warren. Most car stereo's have circuit protection built in.

I'm still wondering about what your initial problem might be. If you checked the connection at the battery and the connection at the transmission, it sure points to a bad alternator. You've probably already done this but test the voltage at the battery with the car running and someone reving the engine up and down. See how the voltage changes if at all. If you see spikes, then the alternator (voltage regulator) is most likely the issue.