Yamaha R1 2004 ServiceManual

							6-13
WATER PUMPCOOL
Order Job / Part Q’ty Remarks
5
6
7
8Water pump seal
Oil seal
Bearing
O-ring1
1
1
1
For installation, reverse the removal 
procedure.
12 Nm (1.2 m
kg, 8.7 ft
lb) 
						

							6-14
WATER PUMPCOOL
NOTE:
NOTE:
NOTE:
EAS00471
DISASSEMBLING THE WATER PUMP
1. Remove:

water pump seal 
1
Tap out the water pump seal from the inside of
the water pump housing.
2Water pump housing
2. Remove:

oil seal 
1

bearing 2
Tap out the bearing and oil seal from the outside
of the water pump housing.
3Water pump housing
3. Remove:

rubber damper holder 
1

rubber damper 2
(from the impeller, with a thin, flat-head
screwdriver)
Do not scratch the impeller shaft.
EAS00473
CHECKING THE WATER PUMP
1. Check:

water pump housing cover 
1

water pump housing 2

impeller 3

rubber damper 4

rubber damper holder 5

water pump seals

oil seal 
Cracks / damage / wear 
 Replace.
2. Check:

bearing 
Rough movement 
 Replace.
3. Check:

water pump outlet pipe
Cracks / damage / wear 
 Replace. 
						

							6-15
WATER PUMPCOOL
NOTE:
CAUTION:
NOTE:
NOTE:
EAS00475
ASSEMBLING THE WATER PUMP
1. Install:

oil seal 
New 1
(into the water pump housing 2)

Before installing the oil seal, apply tap water or
coolant onto its out surface.

Install the oil seal with a socket that matches its
outside diameter.
2. Install:

water pump seal 
New 1
Never lubricate the water pump seal surface
with oil or grease.

Install the water pump seal with the special
tools.

Before installing the water pump seal, apply
Yamaha bond No.1215 or Quick Gasket 
2 to
the water pump housing 
3.
Mechanical seal installer 
4
90890-04078, YM-33221
Middle driven shaft bearing
driver 
5
90890-04058, YM-04058
Yamaha bond #1215
90890-85505
Quick gasket
ACC-11001-05-01
APush down.
3. Install:

rubber damper 
New 2

rubber damper holder New 1
Before installing the rubber damper, apply tap
water or coolant onto its outer surface. 
						

							6-16
WATER PUMPCOOL
CAUTION:
4. Measure:

impeller shaft tilt
Out of specification 
 Repeat steps (3) and
(4).
Make sure the rubber damper and rubber
damper holder are flush with the impeller.
Impeller shaft tilt limit
0.15 mm (0.006 in)
1Straightedge
2Impeller 
						

							7-1
FUEL INJECTION SYSTEMFI
19Atmospheric pressure
sensor
20Fuel injection system
relay
21Engine trouble warning
light
22Lean angle cut-off
switch
23Air cut-off valve
13Coolant temperature
sensor
14Spark plug
15Cylinder identification
sensor
16Pressure regulator
17Battery
18ECU
1Ignition coil
2Air filter case
3Intake temperature
sensor
4Fuel delivery hose
5Fuel tank
6Fuel pump
7Fuel return hose
8Intake air presure sen-
sor
9Throttle position sen-
sor
10Fuel injector
11Catalytic converter
12Crankshaft position
sensor
FUEL INJECTION SYSTEM
FUEL INJECTION SYSTEM 
						

							7-2
FUEL INJECTION SYSTEMFI
7
WIRING DIAGRAM 
						

							7-3
FUEL INJECTION SYSTEMFI
1Main switch
4Fuse (main)
5Fuse (backup)
6Battery
7Fuse (fuel injection)
10Starting circuit cut-off relay
11Neutral switch
12Sidestand switch
13Fuel pump
14E.C.U.
15Ignition coil #1
16Ignition coil #2
17Ignition coil #3
18Ignition coil #4
19Spark plug
20Injector #1
21Injector #2
22Injector #3
23Injector #4
25Sub-throttle position sensor
26EXUP servo motor
27Speed sensor
28Coolant temperature sensor
29Intake air temperature sensor
31Crankshaft position sensor
32Throttle position sensor
33Intake air pressure sensor
34Atmospheric pressure sensor
35Cylinder identification sensor
36Lean angle cut-off switch
43Multi function meter
53Engine stop switch
73Fuse (ignition) 
						

							7-4
30: Lean angle cut-off switch
(latch up detected)
41: Lean angle cut-off switch
(open or short circuit)
50: ECU internal malfunction
(memory check error)
FUEL INJECTION SYSTEMFI
EAS00899
ECU’S SELF-DIAGNOSTIC FUNCTION
The ECU is equipped with a self-diagnostic function in order to ensure that the engine control system is
operating normally. If this function detects a malfunction in the system, it immediately operates the en-
gine under substitute characteristics and illuminates the engine trouble warning light to alert the rider
that a malfunction has occurred in the system. Once a malfunction has been detected, a fault code is
stored in the memory of the ECU.

To inform the rider that the fuel injection system is not functioning, the engine trouble warning light
flashes when the start switch is being pushed to start the engine.

If a malfunction is detected in the system by the self-diagnostic function, this mode provides an ap-
propriate substitute characteristic operation, and alerts the rider of the detected malfunction by illumi-
nating an engine trouble warning light.

After the engine has been stopped, the fault code number appears from the lowest value in order of
precedence on the LCD meter. Once a fault code has been displayed, it remains stored in the memory
of the ECU until it is deleted.
EAS00900
Engine trouble warning light indication and FI system operating condition
Warning light 
indication
ECU’s operationFI operationVehicle operation
Flashing*Warning provided
when unable to start
engineOperation stoppedUnable
Remains ONMalfunction detectedOperated with 
substitute 
characteristics 
in accordance with the
description of the 
malfunctionAble / Unable depend-
ing on the self-diag-
nostic fault code
* The warning light flashes when any one of the conditions listed below is present and the start switch is
pushed.
11: Cylinder identification sensor
12: Crankshaft position sensor
19: Sidestand switch
(open circuit in wire to ECU)
EAS00901
Checking for a defective engine trouble warning light bulb
The engine trouble warning light comes on for 1.4 seconds after the main switch has been turned “ON”
and when the start switch is being pushed. If the warning light does not come on under these condi-
tions, the warning light bulb may be defective. 
						

							7-5
FUEL INJECTION SYSTEMFI
SUBSTITUTE CHARACTERISTICS OPERATION CONTROL (FAIL-SAFE ACTION)
If the ECU detects an abnormal signal from a sensor while the vehicle is being driven, the ECU illumi-
nates the engine trouble warning light and provides the engine with alternate operating instructions
that are appropriate for the type of malfunction.
When an abnormal signal is received from a sensor, the ECU processes the specified values that are
programmed for each sensor in order to provide the engine with alternate operating instructions that
enable the engine to continue to operate or stop operating, depending on the conditions.
The ECU takes fail-safe actions in two ways: one in which the sensor output is set to a prescribed value,
and the other in which the ECU directly operates an actuator. Details on the fail-safe actions are given
in the table below.
FAIL-SAFE ACTIONS TABLE
Fault
Code No.ItemSymptomFail-safe actionAble / unable
to startAble / unable
to drive
11
Cylinder identification
sensorNo normal signals are received from
the cylinder identification sensor.Continues to operate the engine based
on the results of the cylinder
identification that existed up to that
point.
UnableAble
12Crankshaft position
sensorNo normal signals are received from
the crankshaft position sensor.
Stops the engine (by stopping the
injection and ignition).UnableUnable
13
14Intake air pressure
sensor (open or short
circuit) (pipe system)Intake air pressure sensor-open or
short circuit detected.
Faulty intake air pressure sensor 
system.
Fixes the intake air pressure to
101.3 kpa.
AbleAble
15
16Throttle position sensor
(open or short circuit)
(stuck)Throttle position sensor-open or short
circuit detected.
Fixes the throttle position sensor to
fully open.AbleAble
17EXUP servo motor
potention
(open or short circuit)EXUP servo motor potention-open or
short circuit detected.
Turn the EXUP servo motor toward
the open side for 3 seconds and then
stop it.AbleAble
18
EXUP servo motor (lock)A lock of the EXUP servo motor is
detected.
Perform the preventive control
against motor locking.
Perform the lock release operation
twice every 100 seconds.
AbleAble
19Sidestand switch (open
circuit in wire to ECU)Open circuit in the input line of ECU
No.15 terminal is detected when the
start switch is pressed.-- (No start)UnableUnable
20Intake air pressure
Atmospheric pressureDefective values are detected due to
the internal malfunction
Fixes the intake air pressure and
atmospheric pressure to 101.3 kpa.AbleAble
21Coolant temperature
sensorCoolant temperature sensor-open or
short circuit detected.
Fixes the coolant temperature to
60C.AbleAble
22Intake temperature
sensorIntake temperature sensor-open or
short circuit detected.
Fixes the intake temperature to 20C.AbleAble
23Atmospheric pressure
sensorAtmospheric pressure sensor-open or
short circuit detected.
Fixes the atmospheric pressure to
101.3 kpa.AbleAble
33
34
35
36
Faulty ignitionOpen circuit detected in the primary
lead of the ignition coil.
Cut the injection of other cylinder in
the same group with the cylinder that
the error is detected.
(Example: when the #1 cylinder is
detective, cut the injection of #1 and
#4 cylinders, when the #2 cylinder is
detective, cut the injection of #2 and
#3 cylinders).
Turn on the power to the air induction
solenoid to always cut-off the air.
Able
(depending
on the num-
ber of faulty
cylinders)Able
(depending
on the num-
ber of faulty
cylinders)
30
41Lean angle cut-off
switch (latch up
detected) (open or short
circuit)Lean angle cut-off switch-open or short
circuit detected.
Turns OFF the fuel injection system
relay of the fuel system.
UnableUnable
42Speed sensor, neutral
switchNo normal signals are received from the
speed sensor; or, an open or short
circuit is detected in the neutral switch.
Fixes the gear to the top gear.AbleAble
43Fuel system voltage
(monitor voltage)The ECU is unable to monitor the
battery voltage (an open circuit in the
line to the ECU).
Fixes the battery voltage to 12 V.AbleAble
44
Error in writing the
amount of CO
adjustment on
EEPROMAn error is detected while reading or
writing on EEPROM (CO adjustment
value).--
AbleAble 
						

							7-6
FUEL INJECTION SYSTEMFI
Fault
Code No.ItemSymptomFail-safe actionAble / unable
to startAble / unable
to drive
46Vehicle system power
supply (Monitor voltage)Power supply to the FI system is not
normal.--AbleAble
47Sub-throttle servo motor
potention (open or short
circuit)sub-throttle servo motor potention-
open or short circuit detected.
Turn the sub-throttle servo motor
toward the close side for 4 seconds
and then stop it.AbleAble
48
Sub-throttle servo motor
(lock)A lock of the sub-throttle servo motor is
detected.
Perform the preventative control
against motor locking.
(Perform the lock release operation
twice every 100 seconds.)
AbleAble
50ECU internal
malfunction (memory
check error)Faulty ECU memory. When this
malfunction is detected, the code
number might not appear on the meter.--UnableUnable
—
Start unable warningRelay is not turned ON even if the crank
signal is input while the start switch is
turned ON.
When the start switch is turned ON
while an error is detected with the fault
code of No.11, 12, 19, 30, 41 or 50.Engine trouble warning light flashes
when the start switch is turned ON.
UnableUnable
Communication error with the meter
Fault
Code No.ItemSymptomFail-safe actionAble / unable
to startAble / unable
to drive
Er-1ECU internal malfunction
(output signal error)No signals are received from the ECU.–UnableUnable
Er-2ECU internal malfunction
(output signal error)No signals are received from the ECU
within the specified duration.–UnableUnable
Er-3ECU internal malfunction
(output signal error)Data from the ECU cannot be received
correctly.–UnableUnable
Er-4ECU internal malfunction
(input signal error)Non-registered data has been received
from the meter.–UnableUnable