Did you go through the procedure of counting the teeth from the missing tooth to the sensor while the engine is on TDC? There's an offset that needs be entered so the ECU knows where the missing tooth is in relation to TDC. Probably wouldn't hurt to run the toothed wheel logger to see if you're getting a good crank signal. I had to end up putting some pull up reistors in my crank sensor circuit. I'm using the red threaded body sensor from DIY.
