Another alarm question
 

I have a 377 Scorpion with a MEFI3 ECU and I'm getting a steady intermediate beep after reaching about 4000 rpm's the code will not clear until we turn off the ignition. The last service I had, the motor overheated because they did not have the correct flusher attached and they had to replace the water pump impeller, also they had crossed #6 and #8 spark plug wires, we fixed that at night at the launch ramp! Obviously we do not want to take the boat back there. What I have read is that a bad water pump housing will leave the water airated and will cause the water temp sensor to read a high temp. We have checked all levels and connections, next we will pull the sensors off one at a time to isolate the sensor that is giving us the code.
The question I have is, if we had a scan tool attached while running and the alarm comes on will it show the code?