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In my experience the 4.6 was more prone to some oil getting by the valve seals (puff of blue smoke on start up and after idling for a while)...
The 5.4 was more prone to blowing out spark plugs if they weren't torqued properly. Also 5.4 has individual coil on plug (COP) ignition and the coils are prone to failer from time to time (not a big expense).
4.6 is easier to change spark plugs on due to smaller size and not having the COP ignition.
5.4 has better low end torque if you want to tow or off-road. 4.6 might make a touch better mpg.
Rezvani's Latest Post-Apocalyptic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.