I thought about stroking my block aswell but I think it is a bit more expensive and less reliable, I have ben wanting a 5.4 for a long time but that whole intake hight scares me. these companies are finally starting to release after markets for thge 4.6 intake manifolds, and spacers to put them on 5.4's.. so now I am thinkin again.
It has been done. A few people on Corral have done it, it might pay to post over there in their tech section as well. The height of the engine/intake was the biggest headache. Since the Cobra-R had the 5.4 installed, I think you would want to study that also.