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The PC3/5 allows interception of the signals going to the coil/injectors, and modifies the signals according to the map. If the tuner decides the bike needs less fuel at a specific RPM/Throttle position, ( called a "cell") he reduces the number in that cell. If he thinks the bike needs more fuel, he increases the number in that cell. PC3/5 are designed to increase or decrease the pulse width (length of time the injectors are passing fuel) by a percentage, and that percentage is the number placed in the cell. If there is a zero in a cell, then the injector is open for whatever time the factory set it at. If the cell # is positive, say 15, then the PC will lengthen the pulse width by 15% ( 15% richer). If the number is negative, -20, then the injectors will be open 20% less than the ECM asks for, leaning the mix at that point. Timing control is limited to a few % change of the base timing, again, # in the cell.
An other option is TTS/SEST, that allows modification of the ECM software, so that engine parameters, such as actual displacement, injector size, etc can be set to match what has been changed. The actual airflow through the motor can be calibrated via software in the ECM, through the VE tables. Once the VE tables are calibrated, the ECM knows how much airflow is going thru the motor, and add fuel as dictated by the AFR desired table. You also have more timing control, (-4° to +50°, in 1/4° increments) which may be needed for hi comp builds.
Either style can be tuned via Dyno, and, to a small extent, via "butt" dyno, using lap top computers and such, depending how much time & effort you want to put into this project. Some "DIY" guys will ride/tweak-repeat 'till they are happy, some guys simply drop their bike off at the shop with instructions and $.
HTH
Robin
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