They started using the "PI" heads sometime in 99 so you may or may not have them. If you can find the part # on the passenger side head above the exhaust manifold there should be a PI stamped near it if its a pi head of course. It may be very difficult to read due to age, corrosion, grime etc...
I do believe what 1998exp330 stated is correct though so it would be the easiest way to tell. And if you have the intake off..... the non-pi heads have round runners. PI heads have square(ish) runners..lol.
You can install pi heads and intake on non pi motors but this will raise compression to around 10 to 1. This is true on both 4.6 & 5.4 blocks due to the difference in combustion chamber sizes between the heads. Ford increased the volume of the dish (cc's) in the pistons on the PI motors to make up for the difference between the heads.
Then there are windsor vs romeo heads and blocks. They are interchangeable but with some minor differences that need to be addressed. The new ford racing PI heads are romeo and have the 8 thread count spark plug holes!!