Jake, the reduction in VE due to extremely long runner intakes is due to the boundary layer flow loses due to the surface roughness. That's why, as you noted, much more has to be considered when tuning than just one parameter, such as resonant frequencies.
It should be noted that the plastic upper intake manifold has a smoother surface finish than any aluminum casting.
I just got done reading my new book, "Scientific Design of Intake and Exhaust systems" (1972, but amazingly the points it makes explain a great bit of modern engine design!) Quite the in-depth read.
The author rigged up cool apparatus that was capable of reading pressures inside cylinders, exhaust manifolds, and intake manifolds as it changed over fractional rotations of the crankshaft movement during engine running. It explains a lot of very interesting things.
Anyway, I now have a definitive answer as to why too long of an intake runner saps high speed power. What happens with a long intake runner is, early in the intake stroke, as the piston moves down, airflow is lazy with the long runner, due to it's long length and high mass of air, it resists movement initially, and there is a build-up of vacuum inside the cylinder. This build up of vacuum causes the rate of airflow through the intake runner to increase to very rapid rates, and that airflow given enough time (low enough engine RPM) overtakes the expansion of the chamber related from the speed of the piston, and if it has enough time before intake valve closes, can even "supercharge" the cylinder. At high rpms however with too long and narrower runners, the delayed filling of the cylinder during the intake stroke doesn't have enough time to "catch up" with the vacuum generated inside the cylinder at the early part of the stroke.
There was mention that this effect could be reduced by porting: enlarging the diameter of the hole behind the intake valve and the rest of the length of the runner behind.
