Yamaha R1 2004 ServiceManual

							7-7
Engine operation is not normal or the engine trouble warning light is on.
* Engine trouble warning light may not come on even if the engine operation is not normal.
The engine trouble warning light comes on.
Check the fault code number displayed on the me-
ter.
Identify the probable cause of malfunction. (Refer
to the “Diagnostic fault code table”.)
Check and repair the probable case of malfunc-
tion.
Fault code No.
appearFault code No.
disappear
Check and repair.
(Refer to “TROU-
BLESHOOTING DE-
TAILS”.)
Monitor the operation
of the sensors and
actuators in the diag-
nostic mode. (Refer
to “Diagnostic mode
table” in chapter 7)Check and repair.
(Refer to “FAIL-SAFE
ACTIONS TABLE”.)
Perform ECU reinstatement action. (Refer to “Re-
instatement method” in “TROUBLESHOOTING
DETAILS”.)
Turn the main switch to “OFF”, turn the main switch
back to “ON”, and then check if the fault code num-
ber is still displayed.
Erasing the malfunction history:*
The malfunction history is stored even if the main
switch is turned OFF.
The malfunction history must be erased in the
diagnostic mode. (Refer to the “Diagnostic mode
table (Diagnostic code No.62)”)Repairs completed
The engine trouble warning light does not come
on.
Check the operation of following sensors and ac-
tuators in the diagnostic mode (Refer to “Diagnos-
tic mode table” in chapter 7.)
Malfunction of en-
gineDefective sensor
or actuator
Check and repair
the inner parts of
engine. (Refer to
Chapter 5)Check and repair
the corresponding
sensor or actua-
tor.
* Operated when the engine trouble warning light is on.
Fault code 
number displayed
Fault code number not displayed
OKNG
OK
OK
Check the engine condition.
OK NG
01: Throttle position
sensor (throttle
angle)
03: Intake air pressure
07: Vehicle speed pulse
09: Fuel system volt-
age (battery bolt)
21: Neutral switch
30: Ignition coil #1
31: Ignition coil #232: Ignition coil #3
33: Ignition coil #4
36: Injector #1
37: Injector #2
38: Injector #3
39: Injector #4
48: Al system solenoid
53: EXUP servo motor
56: Sub-throttle servo
motor
FUEL INJECTION SYSTEMFI
EAS00904
TROUBLESHOOTING CHART 
						

							7-8
FUEL INJECTION SYSTEMFI
NOTE:
NOTE:
EAS00905
DIAGNOSTIC MODE
It is possible to monitor the sensor output data
or check the activation of actuators without con-
necting the measurement equipment by simply
switching the meter indication from the normal
mode to the diagnostic monitoring mode.
Setting the diagnostic mode
1. Turn the main switch to “OFF” and set the en-
gine stop switch to “OFF”.
2. Disconnect the wire harness coupler from
the fuel pump.
3. Simultaneously press and hold the “SE-
LECT” and “RESET” buttons, turn the main
switch to “ON”, and continue to press the but-
tons 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 CO
adjustment mode “Co” or the diagnostic
mode “dIAG”.
5. After selecting “dIAG”, simultaneously press
the “SELECT” and “RESET” buttons for 2 se-
conds or more to execute the selection.
6. Select the diagnostic code number that ap-
plies to the item that was verified with the
fault code number by pressing the “SELECT”
and “RESET” buttons.

The diagnostic code number appears on the
LCD meter (01-70).

To decrease the selected diagnostic code
number, press the “RESET” button. Press the
“RESET” button for 1 second or longer to auto-
matically decrease the diagnostic code num-
bers.

To increase the selected diagnostic code num-
ber, press the “SELECT” button. Press the
“SELECT” button for 1 second or longer to au-
tomatically increase the diagnostic code num-
bers. 
						

							7-9
FUEL INJECTION SYSTEMFI
NOTE: 7. Verify the operation of the sensor or actuator.

Sensor operation
The data representing the operating condi-
tions of the sensor appears on the trip LCD.

Actuator operation
Set the engine stop switch to “ON” to operate
the actuator.
* If the engine stop switch is set to “ON”, set it
to “OFF”, and then set it to “ON” again.
8. Turn the main switch to “OFF” to cancel the
the diagnostic mode.
To perform a reliable diagnosis, make sure to
turn “OFF” the power supply before every check
and then start right from the beginning. 
						

							7-10
FUEL INJECTION SYSTEMFI
Diagnostic fault code table
Fault
code No.SymptomProbable cause of malfunctionDiagnostic
code
11
No normal signals are received from
the cylinder identification sensor.
Open or short circuit in wiring sub lead.

Open or short circuit in wiring harness.

Defective cylinder identification sensor.

Malfunction in ECU.

Improperly installed sensor.
—
12
No normal signals are received from
the crankshaft position sensor.
Open or short circuit in wiring harness.

Defective crankshaft position sensor.

Malfunction in pickup rotor.

Malfunction in ECU.

Improperly installed sensor.
—
13
Intake air pressure sensor-open or
short circuit detected.
Open or short circuit in wiring sub lead.

Open or short circuit in wiring harness.

Defective intake air pressure sensor.

Malfunction in ECU.
03
14
Faulty intake air pressure sensor hose
system; a hose is detached, causing
constant application of the
atmospheric pressure to the sensor;
or, the hose is clogged.
Intake air pressure sensor hose is detached, clogged,
kinked, or pinched.

Malfunction in ECU.
03
15
Throttle position sensor-open or
short circuit detected.
Open or short circuit in wiring sub lead.

Open or short circuit in wiring harness.

Defective throttle position sensor.

Malfunction in ECU.

Improperly installed throttle position sensor.
01
16A stuck throttle position sensor is
detected.
Stuck throttle position sensor.

Malfunction in ECU.01
17EXUP servo motor potention
circuit-open or short circuit detected.
Open or short circuit in wiring sub lead.

Detective EXUP servo motor (potention circuit).53
18EXUP servo motor is stuck.
Open or short circuit in wiring sub lead.

Stuck EXUP servo motor (mechanism).

Stuck EXUP servo motor (motor).53
19Open circuit in the input line of ECU
No.15 terminal is detected when the
start switch is pressed.
Open circuit in wiring harness (ECU Coupler).

Malfunction in ECU.20
20
When the main switch is turned to ON,
the atmospheric sensor voltage and
intake air pressure sensor voltage
differ greatly.
Atmospheric pressure sensor hose is clogged.

Intake air pressure sensor hose is clogged, kinked, or pinched.

Malfunction of the atmospheric pressure sensor in the
intermediate electrical potential.

Malfunction of the intake air pressure sensor in the
intermediate electrical potential.

Malfunction in ECU.
03
02
21Coolant temperature sensor-open or
short circuit detected.
Open or short circuit in wiring harness.

Defective coolant temperature sensor.

Malfunction in ECU.06
22Intake temperature sensor-open or
short circuit detected.
Open or short circuit in wiring harness.

Defective intake temperature sensor.

Malfunction in ECU.05
23Atmospheric pressure sensor-open or
short circuit detected.
Open or short circuit in wiring sub lead.

Defective atmospheric pressure sensor.

Malfunction in ECU.02
30The motorcycle has overturned.
Overturned.

Malfunction in ECU.08
33
Open circuit is detected in the primary
lead of the ignition coil (#1).
Open or short circuit in wiring harness.

Malfunction in ignition coil.

Malfunction in ECU.

Malfunction in a component of ignition cut-off circuit system.
30 
						

							7-11
FUEL INJECTION SYSTEMFI
Fault
code No.SymptomProbable cause of malfunctionDiagnostic
code
34
Open circuit is detected in the primary
lead of the ignition coil (#2).
Open or short circuit in wiring harness.

Malfunction in ignition coil.

Malfunction in ECU.

Malfunction in a component of ignition cut-off circuit system.
31
35
Open circuit is detected in the primary
lead of the ignition coil (#3).
Open or short circuit in wiring harness.

Malfunction in ignition coil.

Malfunction in ECU.

Malfunction in a component of ignition cut-off circuit system.
32
36
Open circuit is detected in the primary
lead of the ignition coil (#4).
Open or short circuit in wiring harness.

Malfunction in ignition coil.

Malfunction in ECU.

Malfunction in a component of ignition cut-off circuit system.
33
41Lean angle cut-off switch-open or
short circuit detected.
Open or short circuit in wiring harness.

Defective lean angle cut-off switch.

Malfunction in ECU.08
42
No normal signals are received from
the speed sensor; or, an open or
short circuit is detected in the neutral
switch.
Open or short circuit in wiring harness.

Defective speed sensor.

Malfunction in vehicle speed sensor detected unit.

Defective neutral switch.

Malfunction in the engine side of the neutral switch.

Malfunction in ECU.
07
21
43The ECU is unable to monitor the
battery voltage (an open circuit in the
monitor line to the ECU).
Open circuit in wiring harness.

Malfunction in ECU.09
44An error is detected while reading or
writing on EEPROM.
Malfunction in ECU. (The CO adjustment value is not
properly written on or read from the internal memory).60
46Power supply to the FI system is not
normal.
Malfunction in “CHARGING SYSTEM”.—
47Sub-throttle servo motor potention cir-
cuit-open or short circuit detected.
Open or short circuit in wiring harness.

Detective Sub-throttle servo motor (potention circuit).56
48Sub-throttle servo motor is stuck.
Open or short circuit in wiring harness.

Stuck Sub-throttle servo motor (mechanism).

Stuck Sub-throttle servo motor (motor).56
50
Faulty ECU memory. When this
malfunction is detected, the code
number might not appear on the
meter.
Malfunction in ECU. (The program and data are not
properly written on or read from the internal memory.)
—
Er-1
No signal are received from the ECU.
Open or short circuit in wiring harness.

Malfunction in meter.

Malfunction in ECU.

Defective wire connection of the ECU coupler.
—
Er-2No signal are received from the ECU
within the specified duration.
Improper connection in wiring harness.

Malfunction in meter.

Malfunction in ECU.—
Er-3Data from the ECU can not be
received correctly.
Improper connection in wiring harness.

Malfunction in meter.

Malfunction in ECU.—
Er-4Non-registered data has been
received from the meter.
Improper connection in wiring harness.

Malfunction in meter.

Malfunction in ECU.— 
						

							7-12
FUEL INJECTION SYSTEMFI
NOTE: Diagnostic mode table
Switch the meter display from the regular mode to the diagnosis mode. To switch the display, refer to
“DIAGNOSTIC MODE”.

Check the intake air temperature and coolant temperature as close as possible to the intake air tem-
perature sensor and the coolant temperature sensor respectively.

If it is not possible to check it with an atmospheric pressure gauge, judge it by using 101.3 kPa as the
standard.

If it is not possible to check the intake air temperature, use the ambient temperature as reference.
Diagnostic
codeItemDescription of actionData displayed on meter
(reference value)
01
Throttle angleDisplays the throttle angle.

Check with throttle fully closed.

Check with throttle fully open.0 
 125 degrees

Fully closed position (15 
 18)

Fully open position (95 
 100)
02
Atmospheric
pressureDisplays the atmospheric pressure.
* Use an atmospheric pressure gauge to check the
atmospheric pressure.Compare it to the value
displayed on the meter.
03
Intake air pressureDisplays the intake air pressure.
Engine stop switch is on.
* Generate the pressure difference by cranking the engine
with the starter, without actually starting the engine.
Not cranking-atmospheric
pressure

Cranking-intake air pressure It
changes at the value whitch is
smaller than in the atomo-
spheric pressure.
05Intake temperatureDisplays the intake air temperature.
* Check the temperature in the air cleaner case.Compare it to the value
displayed on the meter.
06Coolant temperatureDisplays the coolant temperature.
* Check the temperature of the coolant.Compare it to the value
displayed on the meter.
07
Vehicle speed pulseDisplays the accumulation of the vehicle pulses that are
generated when the tire is spun.(0 
 999; resets to 0 after 999)
OK if the numbers appear on
the meter.
08Lean angle cut-off
switchDisplays the lean angle cut-off switch values.Upright: 0.4 
 1.4 V
Overturned: 3.7 
 4.4 V
09Fuel system voltage
(battery voltage)Displays the fuel system voltage (battery voltage).
Engine stop switch is on.0 
 18.7 V
Normally, approximately 12.0 V
20Sidestand switchDisplays that the switch is ON or OFF. (When the gear is in a
position other than neutral.)Stand retracted: ON
Stand extended: OFF
21Neutral switchDisplays that the switch is ON or OFF.Neutral: ON
In gear: OFF
30
Ignition coil #1After the engine stop switch has been turned from OFF to
ON, it actuates ignition coil #1 for five times every second
and illuminates the engine trouble warning light.
* Connect an ignition checker.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check that spark is generated,
5 times with the engine stop
switch ON.
31
Ignition coils #2After the engine stop switch has been turned from OFF to
ON, it actuates ignition coil #2 for five times every second
and illuminates the engine trouble warning light.
* Connect an ignition checker.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check that spark is generated,
5 times with the engine stop
switch ON. 
						

							7-13
FUEL INJECTION SYSTEMFI
Diagnostic
codeItemDescription of actionData displayed on meter
(reference value)
32
Ignition coil #3After the engine stop switch has been turned from OFF to
ON, it actuates ignition coil #3 for five times every second
and illuminates the engine trouble warning light.
* Connect an ignition checker.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check that spark is generated,
5 times with the engine stop
switch ON.
33
Ignition coil #4After the engine stop switch has been turned from OFF to
ON, it actuates ignition coil #4 for five times every second
and illuminates the engine trouble warning light.
* Connect an ignition checker.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check that spark is generated,
5 times with the engine stop
switch ON.
36
Injector #1After the engine stop switch has been turned from OFF to
ON, it actuates the injector #1 five times every second and
illuminates the engine trouble warning light.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the operating sound of
the injector five times with
engine stop switch ON.
37
Injector #2After the engine stop switch has been turned from OFF to
ON, it actuates the injector #2 five times every second and
illuminates the engine trouble warning light.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the operating sound of
the injector five times with
engine stop switch ON.
38
Injector #3After the engine stop switch has been turned from OFF to
ON, it actuates the injector #3 five times every second and
illuminates the engine trouble warning light.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the operating sound of
the injector five times with
engine stop switch ON.
39
Injector #4After the engine stop switch has been turned from OFF to
ON, it actuates the injector #4 five times every second and
illuminates the engine trouble warning light.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the operating sound of
the injector five times with
engine stop switch ON.
48
AI system solenoidAfter the engine stop switch has been turned from OFF to
ON, it actuates the AI system solenoid five times every
second and illuminates the engine trouble warning light.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the operating sound of
the AI system solenoid 5 times
with the engine stop
switch ON.
50
Fuel injection system
relayAfter the engine stop switch has been turned from OFF to
ON, it actuates the fuel injection system relay five times
every second and illuminates the engine trouble warning
light (the light is OFF when the relay is ON, and the light is
ON when the relay is OFF).
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the fuel injection system
relay operating sound 5 times
with the engine stop
switch ON.
51
Radiator fan motor
relayAfter the engine stop switch has been turned from OFF to
ON, it actuates the radiator fan motor relay five times every
5 seconds and illuminates the engine trouble warning light.
(ON 2 seconds, OFF 3 seconds)
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the radiator fan motor
relay operating sound 5 times
with the engine stop
switch ON.
(At that time, the fan motor
rotates.) 
						

							7-14
FUEL INJECTION SYSTEMFI
Diagnostic
codeItemDescription of actionData displayed on meter
(reference value)
52
Headlight relay 1After the engine stop switch has been turned from OFF to
ON, it actuates the headlight relay five times every
5 seconds and illuminates the engine trouble warning light.
(ON 2 seconds, OFF 3 seconds)
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Check the headlight relay
operating sound 5 times with the
engine stop switch ON.
(At that time, the headlight turns
ON.)
53
EXUP servo motorAfter the engine stop switch has been turned from OFF to
ON, it actuates the servo motor turns to open side and to
close side.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back ON.Turn on the engine trouble
warning light while servo motor
is operated. (Operating angle is
displayed on the LCD meter)
56
Sub-throttle servo
motorAfter the engine stop switch has been turned from OFF to
ON, it actuates the servo motor turns to open side and to
close side.
* If the engine stop switch is ON, turn it OFF once, and then
turn it back on.Turn on the engine trouble warn-
ing light while servo motor is op-
erated (Operating angle is dis-
played on the LCD meter).
60
EEPROM fault code
display
Transmits the abnormal portion of the data in the E2PROM
that has been detected as a self-diagnostic fault code 44.

If multiple malfunctions have been detected, different
codes are displayed at 2-second intervals, and this
process is repeated.(01 
 04) Displays the cylinder
number.
(00) Displays when there is no
malfunction.
61
Malfunction history
code display
Displays the codes of the history of the self-diagnosis
malfunctions (i.e., a code of a malfunction that occurred
once and which has been corrected).

If multiple malfunctions have been detected, different
codes are displayed at 2-second intervals, and this
process is repeated.11  
 50
(00) Displays when there is no
malfunction.
62
Malfunction history
code erasure
Displays the total number of codes that are being detected
through self diagnosis and the fault codes in the past
history.

Erases only the history codes when the engine stop switch
is turned from OFF to ON. If the engine stop switch is ON,
turn it OFF once, and then turn it back ON.00 
 25
(00) Displays when there is no
malfunction.
70Control number
Displays the program control number.00 
 255 
						

							7-15
FUEL INJECTION SYSTEMFI
Cylinder identification sensor
output voltage
When sensor is on
4.8 V or more
When sensor is off
0.8 V or less Tester positive probe 
 white / black
Tester negative probe 
 black / blue
1
2
TROUBLESHOOTING DETAILS
This section describes the measures per fault code number displayed on the meter. Carry out check
and maintenance on items or components that could be a cause of malfunction in accordance with the
order.
When the check and maintenance of malfunctioned part is completed, restore the meter display ac-
cording to the “Restore method”.
Fault code No.:
Fault code number displayed on the meter when the engine failed to work normally. (Refer to “Diag-
nostic fault code table”.)
Diagnostic code No.:
Code number to be used when the diagnostic monitoring mode is operated. (Refer to “DIAGNOS-
TIC MODE”.)
Fault code No.11SymptomNo normal signals are received from the cylinder identification sensor.
Used diagnostic code No. – –
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Installed condition of sensorCheck the installed area for looseness or
pinching.Reinstated by
starting the
2Connected condition of connector
Inspect the coupler for any pins that
may have pulled out.
Check the locking condition of the
coupler.If there is a malfunction, repair it and connect it
securely.
Cylinder identification sensor coupler
Main wiring harness ECU coupler
Sub-wire harness couplerengine and
operating it at
idle.
3Open or short circuit in wiring harness
and / or sub lead.Repair or replace if there is an open or short circuit.
Between sensor coupler and ECU coupler
Blue – Blue
White / Black – White / Black
Black / Blue – Black / Blue
4Defective cylinder identification sensor.Replace if defective.
1. Connect the pocket tester (DC 20 V) to the
cylinder identification sensor coupler terminal
as shown.
2. Set the main switch to “ON”.
3. Measure the cylinder identification sensor out-
put voltage.
4. Is the cylinder identification sensor OK? 
						

							7-16
Crankshaft position sensor
resistance
336 
 504 Ω at 20C (68F)
(between gray and black) Tester positive probe 
 gray 
Tester negative probe 
 black
1
2
12
FUEL INJECTION SYSTEMFI
Fault code No.12SymptomNo normal signals are received from the crankshaft position sensor.
Used diagnostic code No. – –
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Installed condition of sensorCheck the installed area for looseness or
pinching.Reinstated by
cranking the
2Connected condition of connector
Inspect the coupler for any pins that
may have pulled out.
Check the locking condition of the
coupler.If there is a malfunction, repair it and connect it
securely.
Crankshaft position sensor coupler
Main wiring harness ECU couplerengine.
3Open or short circuit in wiring harness.Repair or replace if there is an open or short
circuit between the main wiring harnesses.
Between sensor coupler and ECU coupler
Gray – Gray
Black / Blue – Black / Blue
4Defective crankshaft position sensor.Replace if defective.
1. Disconnect the crankshaft position sensor cou-
pler from the wire harness.
2. Connect the pocket tester (Ω  100) to the
crankshaft position sensor coupler as shown.
3. Measure the crankshaft position sensor resis-
tance.
4. Is the crankshaft position sensor OK?