First off, I'm not into this for the argument. I consider it an excellent discussion, so thanks for keeping it civil.
Second, Ford didn't just "band-aid" their 5.0 intake design. Some serious engineering went into the design, and I'll argue that they did a great job.
Joel really did not get very detailed with his examples, but there is lots of info available:
Long Runner Comparison articles (valid in showing power losses below 5000 rpm in aggressive long runner intakes):
TMoss Porting > Tech Articles > Street Engine Intake Ramblings
Super Intake Shootout - Muscle Mustangs and Fast Fords
Long Runner vs. Box Upper:
AFM - Flow at Last
Probably the best example for the application we're looking at.
AFM - The Runner Volumes
I know this is not the best example, as it is a small displacement/small cammed engine, but it is supercharged and not only turns decent RPM's, but makes decent power. Therefore it is a good example of decent power being made on mild parts. The most noticeable point is that: "no box outperformed the short-runner intakes in average or peak power production."
My whole point is: the intake plays a huge role in the powerband of an engine. While a boxed upper may outperform a long-runner style intake at high RPM's (well above 5000), it will not do so below that point. Realistically, most of us will not build a motor for a street vihicle that will turn more than 6,500 rpm regularly...especially a large journaled 351W. Therefore, a long-runner intake will make more average power under the curve.
Now, if you needed to soften up the torque, due to traction issues and such, this is one way to do it. this is a really old article, but they make some great points towards this part of our subject:
AFM - Manifold Destiny
Port Velocity has to do with air being pulled through the intake by the piston as it moves in the cylinder and creates a vacuum. Air being pulled through a smaller port (into the same sized cylinder) will gain more velocity (speed) as it travels to the cylinder than a larger/shorter port will. What matters, in the case of low-rpm velocity, is what happens as the intake valve closes. Each time the intake closes, there is a rebound effect in the air flow. A longer port will "cushion" this rebound more at the lower rpm levels...resulting in better airflow into the cylinder, and thus more power.
Here's more science into it:
Head Porting Principals