I have never changed the flex plate, but it is conceivable that is the issue. I think the sensor works off it. (Emphasis on the "think" because I am not sure.)
EDIT:
I just checked the factory manual. The crank sensor does run on the flex plate
A few things to check:
- The flex plate should have 2 missing sensor teeth that signals cylinder 1 TDC to the ECU.
- There is a locating pin between the flex plate and the crank flange. That is, the flex plate should only be installed in one orientation relative to the crank. Did the mechanic get this right? If not, it will stuff up the cylinder 1 TDC signalling.
- The correct flex plate part number is 05080065AA.
- There should be a spacer washer between the flex plate and the crank, and another on the outboard side between the flex plate and the bolt hears. The inside one would be important to align the sensor teeth with the sensor.