I did align the sensor with the reference hole and there was no spark.
If the pcm gets the signal from the crank sensor, you will get spark but it will be at the wrong time. What is the distance from top of the sensor to the wheel. It must be really close. I have seen scored sensors by the wheel. Monitoring the pcm for rpm signal will show if it gets the signal. Troubleshooting the problem with timing light will not work. Get some logging device and monitor the PCM. If it sees rpm than you are good, if not the problem is within the sensor position.