If it were a loss of PATS security communication, it would not even crank, so that is not it. Key fob battery or vehicle battery or both could be suspect. Could be low or bad fuel from sitting. Recheck and firmly seat all fuses and relays in the underhood fusebox. Make sure the connectors at the PCM and whatever else you disconnected are good. Can you get codes from the PCM? I would think if it cranks, it can set codes.