A father already accused of setting fire to a car that had his deceased son’s body inside, is facing more charges — including murder — following an autopsy that was completed on the boy, officials said. Manuel Rivera is now charged with murder, second-degree aggravated arson, second-degree endangering the welfare of a child, and second-degree desecration of human remains, the Middlesex County Prosecutor’s Office announced late Friday. Rivera is in critical condition at Robert Wood Johnson University Hospital after he was found outside the car with burns on his body and an undisclosed self-infl…