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In a nutshell, PI heads outflow the non-PI heads. The exhaust valve is 2mm larger and the ports are shaped better to allow more air in/out. The combustion chamber is heart-shaped and the intake ports are square shaped instead of tear drop.
Ford started putting the PI heads on the cars in '99 I believe. I think they started putting them on the 5.4 trucks in '99 as well. The 4.6 truck didn't get them until '00 or '01.
"PI" should be stamped on the outside of the head. But you can easily identify the PI head by the shape of the combustion chamber and intake port.
If you scroll down on the below page, I have pictures of the PI and non-PI heads.
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