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Is it the red LED warning light in the center of the dash that is flashing or is it the temperature or oil warning indicators?
That warning indicates the ECU engine control unit has detected a sensor/sensors in the fuel injection circuit is out of range. If the engine starts and runs then it is not a critical problem and the ECU will use a substitute value for that circuit to allow the engine to continue running. There is a procedure to extract the code or multiple codes in the ECU to determine which circuit or multiple circuits are out of range. Do you feel comfortable in doing a basic procedure to extract the code using a jumper wire on the wire harness?
Locate the diagnostic link connector. It is on the main engine wire harness right side just forward of where the wire for the front cylinder spark plug wires branch of the main harness. It is a red four pin connector with a cap over the end and wraped with electrical tape. Remove the cap. Remove enough of the tape to be able to see the color of the wires entering the connector. The wires you will jumper are the brown and the green/black. It is critical that only these two wires are jumpered. If any other wires make contact it may damage the ECU which is a very expensive part. It is best to fabricate a short loop of wire with the appropriate small female wire connectors to do this.
Once you have a jumper fabricated you need to follow this sequence:
Install the jumper wire in the connector and double check that it is connecting the brown and green/black wires.
Install the lanyard in the handlebar switch.
Push the SET and MODE switches simultaneously for more then 5 seconds and the warning light will begin to flash a series of codes. Each is a set of long then short blinks. There may be more than one code and when all stored codes have been displayed the code pattern will keep repeating.
Let me know what code or codes you get.
Were you able to check this out?