So how do I achieve this? For right now, the arduino is being powered by my laptop, while the dyno setup is powered by a dc source. Either a power supply which connects to an esc which connects to the bldc motor, or a battery that connects to the esc... Their is a six pin sensor harness that goes from the motor to the esc. The pin outs are common ground, sensor C, sensor B, sensor A, temperature, 5v. So this powers the sensor board and the pulses come back on it to the esc. When using the scope I use the common ground and one of the sensor pinouts. But for the pinout going to the arduino I just use the sensor. Should I be putting the common ground from the sensor board to the ground pin on the arduino? I know this would be the case if the entire system was running from the same source, but it isn't. Btw, I do have a 10k resister in series between the sensor lead and the arduino. That helps a lot with the miscounts. It was very random before putting that resistor in.