2004 YAMAHA YZF-R1S wiring

7-29
FUEL INJECTION SYSTEMFI
Speed sensor output voltage
When sensor is on
DC 4.8 V or more
When sensor is off
DC 0.6 V or less Tester positive probe
white
Tester negative probe
black / blue
1
2
Fault code No.42Symptom1 No normal signals are received from the speed sensor.
2 Open or short circuit is detected in the neutral switch.
Used diagnostic code No. 07 (speed sensor)
A1
A4
No. 21 (neutral switch)
B1
B4
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
A1Connected condition of speed sensor
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.
Speed sensor coupler
Main wiring harness ECU couplerReinstated by
starting the
engine, and
inputting the
vehicle speed
signals by
ti thA2Open or short circuit in speed sensor
lead.Repair or replace if there is an open or short circuit.
Between sensor coupler and ECU coupler.
Blue – Blue
White / Yellow – White / Yellow
Black / Blue – Black / Blueoperating the
motorcycle at a
low speed of
20 to 30 km / h.
A3Defective speed sensorExecute the diagnostic mode (Code No.07).
Replace if defective.
1. Measure the speed sensor output voltage.
2. Connect the pocket tester (DC 20 V) to the
speed sensor coupler terminal as shown.
3. Measure the speed sensor output voltage.
4. Is the speed sensor OK?
A4Gear for detecting vehicle speed has
broken.Replace if defective.
Refer to “TRANSMISSION” in chapter 5.
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method.
B1Connected 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.
Neutral switch connector
Main wiring harness ECU couplerReinstated by
starting the
engine, and
inputting the
vehicle speed
ilbB2Open or short circuit in neutral switch
lead.Repair or replace if there is an open or short circuit.
Between switch connector and ECU coupler
Sky blue – Black / Yellowsignals by
operating the
motorcycle at a
low speed ofB3Defective neutral switchExecute the diagnostic mode (Code No.21).
Replace if defective.
Refer to “CHECKING THE SWITCHES” in
chapter 8.low s eed of20 to 30 km / h.
B4Faulty shift drum
(neutral detection area)Replace if defective.
Refer to “TRANSMISSION” in chapter 5.
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7-30
FUEL INJECTION SYSTEMFI
Battery positive terminal
red / black
Battery positive terminal
blue/ yellow1
2
Tester positive probe
red
Tester negative probe
red / blue
3
4 When the leads are disconnected, the voltage
check by the code No.09 is impossible.
NOTE:
Fault code No.43SymptomThe ECU is unable to monitor the battery voltage.
Used diagnostic code No. 09 (fuel system voltage)
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Connected 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.
Starting circuit cut-off relay coupler
(fuel injection system relay)
ECU couplerReinstated by
starting the
engine and
operating it at
idle.
2Malfunction in ECUFuel injection system relay is on.
3Open or short circuit in the wiring harness.Repair or replace if there is an open or short
circuit.
Between battery terminal and ECU coupler
Red / white – Red / white
Red – Blue / Yellow (Main switch and engine
stop switch are on.)
Red – Red / Blue (Fuel injection system
relay is on.)
4Malfunction or open circuit in fuel injection
system relayExecute the diagnostic mode (Code No.09).
Replace if defective.
1. Disconnect the starting circuit cut-off relay
from the wire harness.
2. Connect the pocket tester (Ω  1) and battery
(12 V) to the starting circuit cut-off relay termi-
nals as shown.
3. Does the starting circuit cut-off relay have con-
tinuity between blue / white and black?
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7-31
FUEL INJECTION SYSTEMFI
Fault code No.44SymptomError is detected while reading or writing on EEP-ROM
(CO adjustment value).
Used diagnostic No. 60 (EEP-ROM improper cylinder indication)
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Malfunction in ECUExecute diagnostic code 60
1. Check the faulty cylinder. (If there are multiple
cylinders, the number of the faulty cylinders
appear alternately at 2-second intervals.)
2. Readjust the CO of the displayed cylinder.
Refer to “ADJUSTING THE EXHAUST GAS
VALUME” in chapter 3.
Replace ECU if defective.Reinstated by
turning the
main switch
ON.
Fault code No.46SymptomPower supply to the FI system relay is not normal.
Used diagnostic code No. – –
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Connected 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.
ECU coupler.Reinstated by
starting the
engine and
operating it at
idle.
2Faulty batteryReplace or change the battery
Refer to “CHECKING AND CHARGING THE
BATTERY” in chapter 3.
3The malfunction of the rectifier / regula-
tor.Replace if defective.
Refer to “CHARGING SYSTEM” in chapter 8.
4Open or short circuit in wiring harness.Repair or replace if there is an open or short
circuit.

Between battery and main switch
red – red

Between main switch and fuse (ignition)
brown/blue – brown/blue

Between fuse (ignition) and ECU
red/white – red/white
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7-32
FUEL INJECTION SYSTEMFI
Fault code No.47SymptomSub-throttle position sensor – open or short circuit detected.
Used diagnostic code 56
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Installed condition of sub-throttle position
sensor.Check the installed area for looseness or pinch-
ing.
Check that it is installed in the specified position.
Refer to “THROTTLE BODIES” section.Reinstated by
turning the
main switch
ON.
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.
Throttle position sensor coupler
Main wiring harness ECU coupler
Sub-wire harness coupler
3Open or short circuit in wiring harness
and / or sub lead.Repair or replace if there is an open or short cir-
cuit.
Between sensor coupler and ECU coupler
Black / Blue – Black / Blue
Green / yellow – Green / yellow
Blue – Blue
4Defective sub-throttle position sensor.Replace if defective.
Refer to “THROTTLE BODIES” section.
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7-34
FUEL INJECTION SYSTEMFI
Fault code No.Er-1SymptomNo signal are received from the ECU.
Er-2SymptomNo signal are received from the ECU within the specified duration.
Er-3SymptomData from the ECU cannot be received correctly.
Er-4SymptomNon-registered data has been received from the meter.
Used diagnostic code No. – –
OrderInspection operation item and probable
causeOperation item and countermeasureReinstatement
method
1Connected 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 couplerReinstated by
turning the
main switch
ON.
2Open 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
Yellow / Blue – Yellow / Blue
Black / White – Black / White
3Malfunction in meterReplace the meter.
4Malfunction in ECUReplace the ECU.
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8-3
CHECKING SWITCH CONTINUITYELEC
CAUTION:
NOTE:
NOTE:
EAS00730
CHECKING SWITCH CONTINUITY
Check each switch for continuity with the pocket
tester. If the continuity reading is incorrect,
check the wiring connections and if necessary,
replace the switch.
Never insert the tester probes into the cou-
pler terminal slots. Always insert the probes
from the opposite end of the coupler
1 tak-
ing care not to loosen or damage the leads.
Pocket tester
90890-03112, YU-3112

Before checking for continuity, set the pocket
tester to “0” and to the “Ω
1” range.

When checking for continuity, switch back and
forth between the switch positions a few times.
The terminal connections for switches (e.g.,
main switch, engine stop switch) are shown in
an illustration similar to the one on the left.
The switch positions
a are shown in the far left
column and the switch lead colors
b are shown
in the top row in the switch illustration.
“
” indicates a continuity of electricity
between switch terminals (i.e., a closed circuit
at the respective switch position).
The example illustration on the left shows
that:
There is continuity between red and brown / red
when the switch is set to “P”.
There is continuity between red, brown / blue
and brown / red when the switch is set to “ON”.
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8-10
YESNO 2. Battery

Check the condition of the battery.
Refer to “CHECKING AND CHARGING
THE BATTERY” in chapter 3.
Minimum open-circuit voltage
12.8 V or more at 20C (68F)

Is the battery OK?

Clean the battery
terminals.

Recharge or re-
place the battery.
EAS00739
YESNO
EAS00741
3. Spark plugs
The following procedure applies to all of the
spark plugs.

Check the condition of the spark plug.

Check the spark plug type.

Measure the spark plug gap.
Refer to “CHECKING THE SPARK PLUGS”
in chapter 3.
Standard spark plug
CR9EK (NGK)
Spark plug gap
0.6  0.7 mm (0.0236  0.0276 in)

Is the spark plug in good condition, is it of the
correct type, and is its gap within specifica-
tion?
Re-gap or replace
the spark plug.
IGNITION SYSTEMELEC
NOTE:
YESNO
1. Main and ignition fuses

Check the main and ignition fuses for conti-
nuity.
Refer to “CHECKING THE FUSES” in chap-
ter 3.

Are the main and ignition fuses OK?
Replace the fuse(s).
EAS00737
TROUBLESHOOTING
The ignition system fails to operate (no
spark or intermittent spark).
Check:
1. main and ignition fuses
2. battery
3. spark plugs
4. ignition spark gap
5. ignition coil resistance
6. crankshaft position sensor
7. main switch
8. engine stop switch
9. neutral switch
10. sidestand switch
11. clutch switch
12. starting circuit cut-off relay (diode)
13. lean angle cut-off switch
14. wiring connections
(of the entire ignition system)

Before troubleshooting, remove the following
part(s):
1. seat
2. fuel tank
3. side cowlings

Troubleshoot with the following special tool(s).
Ignition checker
90890-06754
Dynamic spark tester
YM-34487
Pocket tester
90890-03112, YU-3112
EAS00738
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8-13
IGNITION SYSTEMELEC
12. Starting circuit cut-off relay (diode)

Disconnect the starting circuit cut-off relay
coupler from the wire harness.

Connect the pocket tester (Ω
1) to the
starting circuit cut-off relay coupler as
shown.

Check the starting circuit cut-off relay for
continuity.
Positive tester probe

blue / yellow
Negative tester probe

sky blue
1
2
EAS00753
Positive tester probe

blue / yellow
Negative tester probe

blue / black Continuity
1
3
Positive tester probe

sky blue
Negative tester probe

blue / yellow
2
1
Positive tester probe

blue / black
Negative tester probe

blue / yellow No
continuity
3
1
YESNO
Replace the starting
circuit cut-off relay. When you switch the positive and negative
tester probes, the readings in the above chart
will be reversed.

Are the tester readings correct?
NOTE:
13. Lean angle cut-off switch

Check the lean angle cut-off switch.
Refer to “FUEL INJECTION SYSTEM” in
chapter 7.

Is the lean angle cut-off switch OK?
YESNO
Replace the lean
angle cut-off switch.
EAS00754
14. Wiring

Check the entire ignition system’s wiring.
Refer to “CIRCUIT DIAGRAM”.

Is the ignition system’s wiring properly con-
nected and without defects?
YESNO
Properly connect or
repair the ignition
system’s wiring.
Replace the ECU.
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