I would image that pairing sequential cyclinders (1-2 & 3-4) would benifit a motor is due to the energy that effects to the exhaust charge. Since the pulses are sequential, the pulses are dumped one after another as opposed to just dumping everything into one collector. When you space the tubes apart so there are more sequential pulses, the energy from one tube will have a much greater impact on the cylinder it's paired with because it will create a vacuum within the header so that it can draw (suck) more air on the other side (because on of the tubes will be in exhaust while the other is on intake).
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