PCM/ECM: the car's brain.
Are you positive the round grounding connectors in the engine bay were re-connected after the swap? There are two large black wires with a white stripe. One is under the intake tube and hard to see unless you are looking for it. The other is under the battery junction box passing around the battery.
Consider measuring the key off resistance from the PCM pin #25 (Black) wire back to battery negative. Should be low. Post. Also test the BK/WH wires on pin # 3,51,77,103.
If the PCM's ground is bad, it will act as if there is no power. This WILL create a PATS fault.
You are using the correct key right? Remember there's a chip inside the key that the PATS reads on every start up. Do you have an extra key to try?
Also try locking and unlocking the driver's door and locking/unlocking the door with the remote FOB. Sometimes this will reset PATS after a battery disconnect.
Are you aware that almost any locksmith can reprogram a PATS key? This avoids having to tow to a dealer/mechanic.
Any hand held turner that is able to modify the car's tune can disable PATS.
Last edited by wmburns; 09-22-2016 at 11:09 AM.