Here's what the crank-sensor signal should look like going into ECM. Needs a ~10v peak-to-peak difference, or +/- 5v, in order for ECM to distinguish a tooth. The missing tooth indicates TDC.
It actually uses a nifty trick with comparing with IAP/MAP sensor to determine TDC of each cylinder rather than needing a cam-sensor.
Speaking of the IAP/MAP sensor, make sure the hoses going to each cylinder is not out-of-phase, the positions are not interchangeable.