Back in the olden days engines were poorly designed for a lot of reasons including poor science/engineering, lack of available computing power and lack of the target market caring. In this age you could add a pipe, jets, an air filter and go noticeably faster. Starting in the '60s there were advancements being made for general commercial automotive applications. Then we went through the automotive dark ages where engineers grafted new high tech ideas onto old engine designs. During the early days Detroit engines generally made <0.5 hp/CI and world 4 stroke engines made way less than 100 hp/L.
Advances abounded in motorcycle engines during the 80's and car engines during the 90's and power density went way up. Engines are now designed as a system and part of that is designing by paying close attention to VE - Volumetric Efficiency. There are many factors which determine the torque an engine can produce and the RPM at which the maximum torque occurs. However, the fundamental determinant is the mass of air the engine can ingest into the cylinders. For normally aspirated two valve pushrod engines a VE >95% is excellent but with careful tuning of the pulse waves from intake to exhaust it is possible to reach 110%, where the engine can pack in more air than the actual cylinder volume. In DOHC engines VE can hit peaks of 115%. These high VE engines are very peaky, trading lower RPM VE for very high power at high RPMs. Systems can be designed to trade off some of the peak VE to get two smaller VE peaks, or one lower but broader band. The broad band approach is where mainstream engines are tuned for good low-end torque, good throttle response, high mileage, low emissions, and low noise.
When average bike owners without a chassis dynamometer starts drilling holes, swapping exhausts and fiddling with fuel delivery they are taking an optimized system and breaking it in most cases. This is why you want to look for an aftermarket system that has been developed by a tuner business and comes with engineered components that reshape the VE to achieve some new target performance band. Modern engines, especially motorcycle engines with power densities well over 120 hp/L are already highly engineered making it hard to get any significant performance improvements without serious modifications like cylinder heads, NOS or positive pressure like turbos or superchargers.
I spent some time at New England Dragway with a guy that made on the spot modifications to his air box. He went to the strip with air box tuning specifically in mind. His brother drove his tool truck to the track so he could tune the air box and make runs while tracking and compensating for atmospheric changes. He drilled, sawed, plugged and drilled again, ran sans air filter and finally ended up putting an air snorkel on the right side of the air box in addition to the one on the left side. He also had a PC III and used that to try to trim fuel to match the air box mods. The most wildly optimistic 1/4 mile time improvement was ~0.2 seconds after compensating for atmospheric conditions (but, on the other hand, perhaps the rider just got a good run). I was running against him on most of the runs and he never significantly crossed the finish line any farther ahead than at the beginning of the night with a stock system. For what ever reason, his FJR was always faster than mine regardless of the riders.
For those that are still awake: Don't bother modifying the air box.
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