Those rotaries were infamous for rotor seal failure, not surprised if the engine was replaced. Misfire data will show up in mode6. If the crank profile relearn did not stop the flashing MIL (indicates misfire) there must be something else wrong. Possible coil or plug wire issue, don't remember if there was a reflash for misfire but its possible. To spare aggravation, you may want to have the compression checked with a rotary compression checker-before trying any repairs. Does freeze frame offer any clues?

Karl Hering
Consultant
Parsons
Beverly, Massachusetts, USA