The scan tool may say those things, however always verify at the injector or relative sensor.
The VATS might be off but have you checked each module is VIN matched regardless? There is no place for speculated guesses. Get some data to prove yes or no as you move through.
If the engine was swapped, it could be that it was swapped with a bad engine or introduced more bad modules or sensors not in the mix than before.
You could well be at a point where everything is removed and tested independently. Harness continuity is tested pin by pin. Modules reflashed. Key etc, all in succession.