Great thread! Could probably go in the advanced forum. One thing that hasn't been mentioned yet is carburetor size. I think of the link between the combustion chamber and the air outside as a sort of pipeline in which all sizes of the pipe have to compliment each other. For instance, it doesn't make sense to build a 400 small block with 215cc runners and a 600cfm carb. Its just not going to work very well- the sizes of the "pipeline" don't match well. I think carburetor size, as willy's touched on, is really very important for smaller cube engines. Probably the biggest mistake made in hotrodding is over-carbing a 350 Chevy. Very few people have the build-up it takes to make use of 750 CFM in a 350 chevy. The large venturi's are going to slow the air down and make the motor sluggish and sloppy in the low R's (probably the most important RPM range on the street, given that races are won and lost at the starting line).
The way your engine breathes is analogous to blowing through a straw. If you blow through a mcdonald's straw, you can get some pretty good pressure going on the other side if you put your hand in front of it. However the total volume of airflow from such a straw is pretty low- Kind-of like the small, restrictive, low RPM motor that's making good low end power, has great vacuum and small ports. If you tried to blow through a garden hose, however, you'd probably get some pretty weak pressure at the other end- kind of like a smaller cube motor (like a 350) trying to suck air through something like a 750 cfm carb at idle. The total airflow, however is of course much higher (something that a high RPM motor would take advantage of).