I don't think rotating the sensor will change the wave form, it's reading the up and down of the teeth and no teeth spots. It's just an on/off signal. If you turn the key on and wave a wrench in front of the sensor while looking at the signal on a scope it'll turn on/off/on as the wrench passes it or it'll go off/on/off depending which way the sensor is set up. The only way to invert the signal would be to change the sensor for one that triggers the other way from what you have or to make the part that's passing under it the opposite of what you have.
Likely you either have the wrong sensor, the wrong camshaft, or the wrong engine computer. I don't think the sensor would work if the positive and negative were reversed but I'm not sure. Don't test that out on the car, use a benchtop power supply to feed it 5V and ground and probe the output terminal while waving something iron/steel in front of it. A computer power supply works great for this!