If I remember correctly, there's 2 12v power pins that needs to go into the PFC to run properly. On the harness, sometimes, there is only 1 12v power pin and the stock ECU would work with just one power pin but the PFC needs both. You can usually just jumper that pin and run another 12v power to it.
Check the harness and make sure you're getting 12v on those 2 power pins.