Airboxes are great. They keep fuel fumes contained. They make the bike quieter. They help keep water spray under control. They give the carbs a consistant supply of air. The stock jetting is made with the restriction of the airbox in mind. There is only one filter to take care of. They give you a place to dump the crankcase vent. So they really are great things. In the grand scheme of things at least. Notice I didn't say they made more power.
Joe, I'm only not a member of the pod crowd because I think you can get more filter aera with a simple airbox.

More filter aera means less intake restriction... you know the rest. And for those not willing to fabricate, pods are the next best thing.
I still stand by my air box, and if i do any engine modifications to the bike, it will be to machine down the crank shaft/fly wheel.
To what end? Reducing rotating weight does not give you more horsepower. Yes, it can help with acceleration, but a 30hp motor is making 30hp weather or not it's got an additonal 5lbs of flywheel weight.
unfortuneately the air pump analagy, while beautiful in it's implicity, is kinda like a dumb blond. It's showing you what you want to see.
However, the air pump analogy is incredably accurate. We will get back to that in a moment because your next statement trumps this one.
oh, and by the way, more air and gas DOES NOT EQUAL MORE POWER!
the rate of volumetric expantion with increase temperature is quite slow at low temperatures, and fast at high temperatures. high temperatures are reach when air/gas, under the correct pressure, is allowed to complete its combustion, and then is exhausted just before it does. so in fact is it better to run a HOT engine, rather than one with too much gas.
So an engine works by extracting energy from fuel. That energy is expressed as heat. The more fuel you can completely burn, the more power your engine will make. To burn more fuel, you need more air. If you remove restrictions in the intake path, you have higher pressure trying to pass the intake valve. More air will get into the cylinder. That is, your pump will pump more air. Given you rejet properly, you will make more power. This is true for all internal combustion engines. 2 stroke, 4 stroke, wankel, turbine, turbocharged, supercharged... whatever.
Though it's very hard to decipher what you were trying to get at with your heat related discussion.. I'll try to pick the best parts I can from it. A fuel air mix does burn better when compressed. You get more power from that mixture if you start it off at a cooler temprature. (this is why cool air intakes help.. and they really do. And why things like DFI are really neat.. but that's for another discussion) While your statement that it's better to have a HOT engine than a cold one, isn't exactly true, it is close. The point your engine makes the hottest EGT, and (in our air cooled machines) the highest cylinder head temps is almost smack dab between the two points where we would like to run our engines. A little rich of that point and you have your peak power, a bit lean of it, you'll have peak BSFC. (and were you'll get the best fuel economy to boot!) Both spots are quite warm, to say the least.
That set of statements comes right back to the "an engine is an air pump" thing. Again, the more fuel you can burn, the more power you'll make. To burn more fuel, you need more air. To get more air, you need to make your pump move more air. Be it by turning the motor faster, making the intakes different shapes or sizes, improving scavenging, changing the carburators, changing the intake path in front of those, or pumping the air in with a turbo or supercharger.
If the air pump thing isn't true..... What is? Now that I just read your first post in this thread, I really need to suggest you do some reading. Just about any engine tuning book in your local libaray will definitely get you going down the right path. I really don't know where you're getting your ideas from.