Here are some notes that I have on the subject. I swapped a 1999 5.4 in place of my 4.6. Not difficult at all.
Notes for 4.6 to 5.4 swap Revised 09 March 2008
Exhaust: The collectors on the exhaust manifolds are set at different angles and locations. The 4.6 exhaust will not bolt up to 5.4 manifold. You will need to have a mufflar shop modify your 4.6 exhaust to match up.
Ignition: All 5.4 engines use Cop ignition. . 2000 and later 4.6 use COP ingnition. 1997-99 4.6 engines use coil packs. It is easier to wire your 5.4 using the harness from the 4.6 and the 4.6 ignition coil packs if applicable. If you use the 4.6 Coil pack ignition you will have to fab a bracket for the driver side coil pack.
Engine harness: The IAC harness must be relocated to the rear of the throttle body elbow. The oil sender wire on the 4.6 is too short so it must be extended. All 97-00 4.6 engines use some sort of intake manifold runner control valve. Remove it from the 4.6 and plug it into the 4.6 harness and bolt it to the engine some where out of the way. Note you can get a tune to remove its function and eliminate it all together. All 97-98 4.6 engines use an engine coolant temp sensor. Some use 2. None of the 99+ 5.4s use any. You will have to tap the intake manifold crossover pipe to fit the sensor. Some 4.6 engines (97-8) have two sensors.
Transmissions: the 4.6 and 5.4 have the same bellhousing bolt pattern. That means that all the transmissions will bolt up. All the 5.4 engines have 8 bolt crankshafts. Some 4.6 engines (ROMEO ENGINE) have 6 bolt cranks. You will need the flex plate from the 5.4.
Manual transmissions: If you don’t have an 8 bolt flywheel a flywheel from a 1997-8 4.6 Windsor engine will work. As it has 8 bolts it will bolt right up to the 5.4 crank. Remove the flex plate spacer and install a pilot bearing from a 4.6.
Tuning: It is best to have a custom tune done to accommodate the extra displacement of the 5.4.
You should be able to use the 4.6 MAF as any competent tuner can adjust for it. It is always best to discuss this with your tuner.
The 97-98 99 4.6 uses a 2 wire knock sensor. The 97-98 5.4 has 3 wires of which one is a ground. Both have a Yellow /red wire to pin 57 on PCM.
1997-98-99-2000-01 Yellow/red to 57 on PCM 4.6 Same for 5.4.
97-98 Pin 91 feeds power for 4.6 and other components. Same for 5.4
1999- 2000-01 Pin 32 for power. Same fore 5.4
2002+ Cannot confirm.
Accessories: Some engines have 8 rib serpentine belts and some have 6. Be sure to check so that your accessories have the correct pulley.
Misc: Both engines use the same engine mounts and their location on the block are also the same so your old ones will fit. Unbolt and place aside the AC and PS. You need to remove the intake manifold for the engine to come out. Yes there are 3 bolts on the starter.
Jean Marc Chartier