For the average joe, installing a 5.4 is a LOT of work. Sure it can be done. I have read several post regarding it. I also think it is telling that the cars are SOLD after doing sooo much work.
If it was up to me, I spend the $$'s on a name brand super charger kit. It will bolt up and will work as advertised.
If you had $$'s to burn, I suspect the breathing problem could be solved by a supercharger. But then way not build a stroker 4.6? If that is not enough, add a supercharger. Again, not tons of custom work with the possibility of a less than desireable outcome.
A 5.4 is *technically* a stroked 4.6. They share the exact same pistons. Stroking a 4.6 and staying N/A brings the exact same breathing problems that the 5.4 has with the exception of the extra weight on the nose.
Just some food for thought. A comparison done a few years ago using completely stock parts and staying with the stock compression ratio, the 5.0L stroker LOST 17 RWHP and saw a 12 RWTQ gain. The power/torque band was moved lower in the RPM band. The 4.6L made more RWHP and RWTQ after 3500 RPM.
Personally if you want an increase in displacement with desirable gains especially if staying N/A with a modular V8, then the ONLY way to do it is with a larger bore.
Even though I have a N/A Big-Bore 4.6L( 5.0L ), it would be far easier to see a gain in HP with a SC and it is far more cost effective.