The knock sensors are in the valley cover, and are notorious for crapping out when removed.
The alternator is a new one from AutoZone and has to do with (PCM) uses the generator field duty cycle signal circuit to monitor the duty cycle of the generator. The generator field duty cycle signal circuit connects to the high side of the field winding in the generator. A Pulse Width Modulated (PWM) high side driver in the voltage regulator turns the field winding ON and OFF. The PCM uses the PWM signal input to determine the generator load on the engine. This allows the PCM to adjust the idle speed to compensate for high electrical loads. It still charges just fine and has never been a issue.