Wow, I should have kept up on this post, sorry guys!
Ok, this is how it works from how I understand it. First and foremost, this is the most important formula you will need in understanding the basics of how a gas (air) acts under different circumstances; pV=nRTWhere:p is the ABSOLUTE pressureV is the volume of the container holding the gasn is how much gas, which is measured in molesR is the gas constant, which is a number I don't remember off the top of my head right nowT is the temperature of the gas measure in Kelvin IIRC.
OK, I just wiki'd it. Less typing this way...
http://en.wikipedia.org/wiki/Ideal_gas_law
As for the Venturi effect, it sort of applies, here, but not really. Yes, we are effecting the pressure of the gas flow by varying the diameter of the runners, but we aren't really using the venturi effect to introduce any sort of fluid or gas into the air stream. If the system was carburated, it would be a very different story as a carburator wouldn't function without the venturi effect.
As for the plenum and intake runners, I THINK you could port them smooth as they don't need to keep fuel in suspension, but something tells me that they need to be rough because the temperature of the gas is VASTLY different than that from the exhaust. From what I understand, the slightly rough surface creates a small area of turbulence at the surface of the runner, that actually lets the larger column of air travel faster than it would if the port were completely smooth. The exhaust is different because the increased temperatures causes the air to become more viscous and so the port needs to be as smooth as possible.
Also remember that all of these principles were based on steady state flow. A piston engine IS NOT a steady state air flow device. And those pluses and waves have a BIG impact on how the air flows into and out of the combustion chamber.
At least that is the way that I understand it. I don't exactly have a degree in thermodynamics.