5.4 is a bigger engine than a 4.6 so it should have more low end torque and hp. lt costs less to modify because of the bigger size. IMO, 5.4 is better.
Actually, the Cobra R came with a 5.3988... lol, j/k. I think the 5.4 is great, but wouldn't gas milage suffer a bit more? And also, I would think a 5.4 would be a little harder to maintain. But I just drive, I don't work on cars. <IMG src=smileys/smiley1.gif border="0">