some very good points in this article. very well worded chris. I tried to give you rep.. but apparently I have to give more rep to other people before I can give some to you again.
A few others that can be added to the list, is the pulse rebound that happens after a valve shuts.
On the 05+ tacomas the air surge tank has a butterfly valve that adjusts the runner length to optimize that pulse rebound to provide optimal efficiency through the full RPM band. This is essentially the theory behind the throttle body spacer, as the throttle body will act as the rebound point on the intake, where the collector is the rebound on the exhaust end.
Then we can talk about backpressure and the importance of proper header design.
You can also dive into diameter changes, port matching, and the Bernoulli's Principle as well (purpose behind mandrel bends in exhaust).
Lots of fun stuff... doesn't everybody just love to learn about the engineering that goes into what we all assumed was just "some path to get air from outside to the motor, and the the motor back to the outside"
PS.. what happened to getting this as a sticky..