P1260 will indicate a 'key not recognized' situation.
Also be aware that an IMMOBILIZATION SETUP is required EVERY TIME an ECM is introduced to a different car.
Once configured to the car, you cannot put the old one back without ANOTHER IMMO SETUP. (only one ECM to a car recognized)

If you are going to require an IMMO SETUP, then the same equipment can be used to configure KEYS to the car.

Pick one!!!
IMMO SETUP or configure keys. You only need one with the original ECM.

There are more modules on the CAN bus that were not replaced but I never tried to fool the network the way you did with several modules but not ALL.
The INSTPK, TCM, Selector Lever Illumination Module and ABS are VCATS 'plug&play but the ECM need configuring to the CAN bus.

If you leave the replacement ECM in, then you MIGHT need keys configured but definitely an IMMO SETUP.