The PI heads from the 99-04 Mustangs outflow the 94-98 heads and when paired with the correct PI cams and intake manifold, they deliver a huge increase in horsepower and torque. This will also bump up your compression to 10.5:1. One key factor when sourcing these parts is the difference in Romeo and Windsor heads. A quick way to find out which you have is Romeo has 11 bolts and the Windsor has 13/14 bolts. The Ford Racing head changing kit will include all of the necessary head gaskets, exhaust gaskets, head bolts, and rubber seals you need to make the swap.
The 1994-1998 Mustang intake has a different design than the later 99-04 intake manifold making them incompatible with the PI heads. Luckily, this is easily solved by purchasing a new 99-04 Mustang PI intake manifold from LMR. This new intake features a longer aluminum crossover that extends the hook up to the thermostat housing. This will require a new hose kit and a new alternator bracket, both available at LMR as well.
If your PI heads did not come with the camshafts pre-installed, you will need to source camshafts from 1999-2004 SOHC cams, also known as PI cams. The 1996-1998 camshafts have .482 lift and 204/208 duration while the newer PI cams have a .535 lift and 192/184 duration.
These are the basic guidelines of the swap. Each swap could be different per application and additional parts may be needed.