You will only realize that potential if you add a SC or Turbo when comparing a 5.4 2V engine to a 4.6 2V engine. I have yet to see a 5.4 2V with all of the best parts out there equal a 4.6 2V with the same parts in N/A trim. I have seen a lot try though.
What I am saying is that you can put everything on a 5.4, ported heads, good cams, good intake, etc., and buddy down the street that has those parts on his 4.6 will make more power and run faster in the 1/4 than your car. If you are staying N/A and want a 5.4, you need the 4V heads or it is not worth it. Staying N/A in 2V form, you will be moving backwards doing the 5.4 swap.