If you had to replace the PATS module, I agree. The transceiver got fried which is connected to the ignition. This part is supposed to be the cheapest part to replace and it requires no programming as well. The transceiver is only a signal that tells the PCM is the right key. Its only a signal piece therefore no programming necessary.
What happened was a "Quote un Quote" Experienced electronics technician knew how to test wires and he wanted to test the wire in the headlight switch which is the (Black and Orange) wire which happened to be the signal wire to the Transceiver from PATS. He thought is was a ground. The Grey wire is the smallest wire which went to the door jamb switch. He thought is was the Power wire. 94-95 models have thick grey wires as 12v positive. Mine happened to be a thick brown wire. He touched the Grey wire and orange wire together which put 12 volts to the signal wire and fried the Transceiver piece. "An idiot he is. Everyone knows any time you test a wire, you always ground yourself to the chassis of the car. Do not touch both wires.
Hes the Link to show the wires of the PATS system. If you see the black and orange wire going to the Transceiver from PATS, that would be the signal wire. If you put 12v to that wire can you see it frying the Transceiver?
LINK TO 98 MUSTANG PATS Ford Questions - 98 mustang wont start . theft lamp on dash flashing rapid - JustAnswer
Remember, he fried the signal wire which is black and orange which was in the headlight switch connector piece HE touched the door Jamb power wire (Grey) with the positive probe and touch the black and orange wire (Transceiver signal) with the negative probe. This put 12v to a signal wire which fried the wire