Did you swap the power and ground leads at the coil pack? This would hopefully tell you a few things:
1) Your coil is bad, if the 2/3 coil fires when connected to 1/4 ECU/+12V
2) Your 1/4 wiring is compromised
3) Bad news, but your ECU may be damaged.
Regardless, do connect the Good Coil to the Suspect 1&4 connectors and verify operation as you have done before!
INSPECT ALL connection under the tank. Also there is the Diagnostic test which allows you to fire 1/4 and 2/3 coils.... --> post 6
DIAGNOSTIC MODE, ERROR CODES, SENSOR OPERATION
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SYSTEMS that can be Verified:
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To activate, turn Engine Run switch from OFF to ON while mode is selected.
01: Throttle position sensor (throttle angle)
30: Ignition coil #1, #4
31: Ignition coil #2, #3
36: Injector #1, #4
37: Injector #2, #3
48: AI system solenoid
51: Radiator fan motor relay is activated every 5 seconds.
52: Headlight relay is activated every 5 seconds (2 seconds ON, 3 seconds OFF) - 2003+ model only.
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The ECM has the ability to verify some of the sensors and switches on the vehicle. When placed into diagnostic mode it can also display inactive error codes and some history as well as test both the ignition coils and the fuel injectors. For most of these tests, the FSM instruction the user to disconnect the Fuel Pump power (Green connector under the fuel tank).
Setting the diagnostic mode S2 Models:
1. Turn the main switch to “OFF” and set the engine stop switch to “STOP”.
2. Disconnect the wire harness coupler from the fuel pump (GREEN connector).
3. Simultaneously press and hold the “SELECT” and “RESET” buttons, turn the main switch to “ON”, and continue to press the buttons for 8 seconds or more.
• All displays on the meter disappear except the clock and tripmeter displays.
• “dIAG” appears on the LCD meter.
4. Press the “SELECT” button to select the C0 adjustment mode “C0” or the diagnostic mode “dIAG”. US bikes will only display "dIAG", unless a jumper wire is grounding a pin in the harness to enable C0/C1 fuel trim adjustments.
5. After selecting “dIAG”, simultaneously press the “SELECT” and “RESET” buttons for 2 seconds or more to execute the selection.
6. Set the engine stop switch to “OFF”.
7. Select the diagnostic code number that applies to the item that was verified with the fault code number by pressing the “SELECT” and “RESET” buttons.
NOTE:
The diagnostic code number appears on the clock LCD (01–70).
• To decrease the selected diagnostic code number, press the “RESET” button. Press the “RESET” button for 1 second or longer to automatically decrease the diagnostic code numbers.
• To increase the selected diagnostic code number, press the “SELECT” button. Press the “SELECT” button for 1 second or longer to automatically increase the diagnostic code numbers.
8. Verify the operation of the sensor or actuator.
• Sensor operation
The data representing the operating conditions of the sensor appears on the trip LCD.
• Actuator operation
Set the engine stop switch to “RUN” to operate the actuator.
NOTE:
If the engine stop switch is set to “RUN”, set it to “OFF”, and then set it to “RUN” again.
9. Turn the main switch to “OFF” to cancel the diagnostic mode.