ram, if I might take this a little further...
Please do! 
The pressure waves are similar (albeit a much more complicated dynamic) to the pressures an exhaust pipe. So lets look at that... You know when the pipes are small, they are restrictive because of volume and temperature and surface friction, and that is with the predominant push provided by the piston. This is especially true with street exhaust limited by room for headers or manifolding. You know a drop in diameter, or sudden drop in size creates a bad flow situation because of the turbulence and interuption in the flow of these waves. And that's true with a piston pushing it thru. So back to the intake port... A few extra things are working with the piston to get the mixture in efficiently. The harmonic waves (pressure waves) of varying frequencies, the inertia of the mixture itself caused by the port speed, the smooth transitions between components, the friction reduction of the surface finish... The port from a physics standpoint, extends from the base of the carb or throttle body to the intake valve seat. It's one system including a plenum area, a total length, and a volume.
Ok cool, so I am getting this right.
If you seperate out one cylinder, you can easier see the effect a change in matching parts can make.
Interesting that you mention the single cylinder example as that was what got me interested in Hot Rodding when I was 13. I had a mini bike with a 5hp Briggs & Stratton engine and different lengths and diameter of exhaust pipe made drastic changes to where power output peaked.
Me being me, I had to find out why so I went got "The Design and Tuning of Competition Engines" by Phillip H. Smith. There are some excellent explanations of wave tuning for both intake and exhaust and everything started to make sense.
Run a small intake with longer runners, and a small port, and you have a system designed for torque. It makes use of the earlier harmonic waves to push the mixture down to the port, and the inertia is greater and the friction is lowest in a small fast port. Stick a large port large plenum intake on it, and the change between the sizes effectively ruin those waves' effects. It becomes a choke and you will lose tq and hp as those waves are disturbed so far that they cannot help anymore and the piston is the only part supplying energy to move the mix in. Similarly, a small, long port, small plenum intake, combined with a large volume port, and the waves get a good start, and then loss energy when the larger volume is encountered.
This is the mismatch I was speaking of and you hit it right on the head. Just like how a dented/ballooned out pipe will put a brass instrument like a tuba or a trumpet out of tune.
In addition, there is a pressure wave that helps force the mix down the port when the valve is closed. In a small port, that wave stays fairly strong, and the length of the port gives room for the mix to fill before the valve opens. It's part of the "sonic tuning" in long rams mopar used. If that particular wave started up a large port, then hit the size change, it will also be reduced. So the mix goes into the intake, hits the port, the change in size slows it, the waves fall apart, and the power level drops as a result because cylinder filling is reduced. Unfortunately, with regard to physics, there is only one perfect port for every engine at a certain rpm and camshaft design. So the problem becomes what rpm range does the port need to work over and you go from there.
