That link shows a 2 valve 4.6. All the 04+ 5.4 engines are 3 valve.

Regardless.
The engine bolts up to the transmission so no problem there. To utilize the Variable Cam Timing And the Charge Motion Control you will need a 04+ PCM. For that to function properly you will need all 3 of the harnesses, Engine, Transmission, Body. I am not sure about the tranny harness but if the body harness is not connected to an 04 instrument cluster/dash it will set codes.

If you want to run the engine like a 2 valve without the VCT there is no EGR so you will need to work that into the system. The VCT cam phasers will have to be locked down. You can purchase the parts aftermarket. The Charge Motion Control could possible be controlled by the IMRC but you would need to check with your tuner. BTW you will need to tune the PCM for all these changes.

One last thing. Check the spark plugs on the 3 valve engine while it is out of the truck. Much easier to repair out of the truck.

Regards

Jean Marc Chartier