I would start with the wiring diagrams to see how much work it would take to make the ECM and any other in body computers either think it is a big Cobra or if it will be OK with a split personality.
Then I’d want the Cobra motor, complete with computer, sensors and uncut harness for the entire car. Then I would start using the wiring diagrams for both vehicles so I could plan out where to start labeling and swapping in the engine harness and whatever else was needed for the dash and security system.
Are you sure putting in a 5.4 truck motor and getting a tune might be easier? If both motors have similar heads and sensors, it might be a lot quicker and provide a better torque curve to fit the vehicle.