I did it also. When I rebuilt my motor I put PI heads on in place of the non-PI.
The only issues you have to be careful of are the increase in compression. When you bolt PI heads onto the Non-PI pistons you CR will go above 10to1. I was replacing my pistons at the same time so I used 16CC (vs18cc) pistons. With the thicker head gasket I should have come out with close to stock CR (maybe a little higher).
This becomes more of a problem because you are supercharged. You can have the head shop machine the combustion chamber to open it up but they need to know what they are doing.
Good luck and always have fun.

WLF

 

Forgot to mention, the chains, tensioners, front cover, gears, everything on the motor fit just fine. I got 5.4 heads from a 2001 Lightning (WINDSOR) and had them rebuilt with spark plug inserts. I got a 2003 intake manifold off a Romeo engine and it also fit.
My orriginal 4.6 had Windsor heads so I wanted the valve covers to fit without problem.

 

See thats the thing with the PI heads More Compression on my motor wich is already supercharged with boost ranging from 8-10 lbs. I am wondering if my machine shop can open up the combustion chamber enough with a supercharger. I could lower the boost down to 6 lbs but then I would be back where I started. The truck only has 84,000 miles on and runs like new. I plan on keeping this truck for a long time, i just don't have th desire to by a new one. So I will just buy one thing at a time Heads, Intake, Gasket kit, Pistons, Rods etc. and just rebuild the thing when the time comes.