It is possible that the tone wheel on the flex plate has excessive radial runout causing the sensor to not get a good signal intermittently. You would need to either pull the engine or transmission to inspect the Flex Plate more carefully, just replace it or try playing with the airgap for the crank sensor.
I've found in the past that even though the crank sensor is not adjustable, you can either slightly grind down the sensor where it mounts at or add a thin shim to play with the air gap to see if you can get a better signal.. Try bringing the sensor a bit farther from the flex plate first to see if things get better, if that doesn't help, then grind down the sensor mounting area a bit and remount it and see if things get better. If neither solutions help, you will have no choice but to pull the eng or trans for close inspection of the flex plate.
Keep me posted and let me know if you have any additional questions...
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