You are true about the crankshaft position sensor. I just talked about ultra fine tuning when you screw it on the timing cover. You can move it about 0.04", but it's not very important.
I suggest you to try the timing light test to see if the marks on the pulley is aligned with the one on the timing cover. It could indicate a misconfigured PCM.
I think that your PCM don't have the factory setting. This is possible.