Yamaha FJR1300(S) Manual

2004
FJR1300(S)
FJR1300A(S)
5JW1-AE5
SUPPLEMENTARY
SERVICE MANUAL

FOREWORD
This Supplementary Service Manual has been prepared to introduce new service and data for the
FJR1300(S)/FJR1300A(S) 2004. For complete service information procedures it is necessary to
use this Supplementary Service Manual together with the following manuals.
FJR1300(N) 2001 SERVICE MANUAL: 5JW1-AE1
FJR1300(P) 2002 SUPPLEMENTARY SERVICE MANUAL: 5JW1-AE2
FJR1300(R)/FJR1300A(R) 2003 SUPPLEMENTARY SERVICE MANUAL: 5JW1-AE4
FJR1300(S)/FJR1300A(S) 2004
SUPPLEMENTARY
SERVICE MANUAL
© 2003 by Yamaha Motor Co., Ltd.
First edition, September 2003
All rights reserved.
Any reproduction or unauthorized use
without the written permission of
Yamaha Motor Co., Ltd.
is expressly prohibited.

EAS00002
NOTICE
This manual was produced by the Yamaha Motor Company, Ltd. primarily for use by Yamaha deal-
ers and their qualified mechanics. It is not possible to include all the knowledge of a mechanic in
one manual. Therefore, anyone who uses this book to perform maintenance and repairs on Yamaha
vehicles should have a basic understanding of mechanics and the techniques to repair these types
of vehicles. Repair and maintenance work attempted by anyone without this knowledge is likely to
render the vehicle unsafe and unfit for use.
Yamaha Motor Company, Ltd. is continually striving to improve all of its models. Modifications and
significant changes in specifications or procedures will be forwarded to all authorized Yamaha deal-
ers and will appear in future editions of this manual where applicable.
NOTE:
@
Designs and specifications are subject to change without notice.
EAS00004
IMPORTANT MANUAL INFORMATION
Particularly important information is distinguished in this manual by the following.
The Safety Alert Symbol means ATTENTION! BECOME ALERT! YOUR
SAFETY IS INVOLVED!
Failure to follow WARNING instructions could result in severe injury or death to
the motorcycle operator, a bystander or a person checking or repairing the
motorcycle.
A CAUTION indicates special precautions that must be taken to avoid damage
to the motorcycle.
A NOTE provides key information to make procedures easier or clearer.
WARNING
CAUTION:
NOTE:

EAS00007
HOW TO USE THIS MANUAL
This manual is intended as a handy, easy-to-read reference book for the mechanic. Comprehensive
explanations of all installation, removal, disassembly, assembly, repair and check procedures are
laid out with the individual steps in sequential order.
1The manual is divided into chapters. An abbreviation and symbol in the upper right corner of
each page indicate the current chapter.
Refer to “SYMBOLS”.
2Each chapter is divided into sections. The current section title is shown at the top of each page,
except in chapter 3 (“PERIODIC CHECKS AND ADJUSTMENTS”), where the sub-section title(s)
appears.
3Sub-section titles appear in smaller print than the section title.
4To help identify parts and clarify procedure steps, there are exploded diagrams at the start of
each removal and disassembly section.
5Numbers are given in the order of the jobs in the exploded diagram. A circled number indicates a
disassembly step.
6Symbols indicate parts to be lubricated or replaced.
Refer to “SYMBOLS”.
7A job instruction chart accompanies the exploded diagram, providing the order of jobs, names of
parts, notes in jobs, etc.
8Jobs requiring more information (such as special tools and technical data) are described sequen-
tially.

EAS00008
SYMBOLS
The following symbols are not relevant to
every vehicle.
Symbols 1to 9indicate the subject of each
chapter.
1General information
2Specifications
3Periodic checks and adjustments
4Chassis
5Engine
6Cooling system
7Fuel injection system
8Electrical system
9Troubleshooting
Symbols 0to Gindicate the following.
0Serviceable with engine mounted
AFilling fluid
BLubricant
CSpecial tool
DTightening torque
EWear limit, clearance
FEngine speed
GElectrical data
Symbols Hto Min the exploded diagrams
indicate the types of lubricants and lubrication
points.
HEngine oil
IGear oil
JMolybdenum disulfide oil
KWheel bearing grease
LLithium soap base grease
MMolybdenum disulfide grease
Symbols Nto Oin the exploded diagrams
indicate the following.
NApply locking agent (LOCTITE®)
OReplace the part
12
34
56
78
90
AB
CD
EFG
HIJ
KLM
NO
GEN
INFO
SPEC
CHK
ADJ
CHAS
ENG
COOL
FI –+
ELEC
TRBL
SHTG
T
R
.
.
EGM
BLS M
LT
New

CONTENTS
GENERAL INFORMATION ..............................................................................1
FEATURES ...............................................................................................1
OUTLINE ...............................................................................................1
FI SYSTEM ...........................................................................................2
SPECIFICATIONS ............................................................................................3
GENERAL SPECIFICATIONS ..................................................................3
ENGINE SPECIFICATIONS ......................................................................3
ELECTRICAL SPECIFICATIONS .............................................................4
PERIODIC CHECKS AND ADJUSTMENTS ....................................................5
INTRODUCTION .......................................................................................5
PERIODIC MAINTENANCE AND LUBRICATION CHART .......................5
SEATS AND FUEL TANK .........................................................................7
FUEL TANK ..........................................................................................7
REMOVING THE FUEL TANK ..............................................................9
AIR FILTER CASE ..................................................................................10
FUEL INJECTION SYSTEM ...........................................................................12
FUEL INJECTION SYSTEM ...................................................................12
WIRING DIAGRAM (FJR1300) ...........................................................13
WIRING DIAGRAM (FJR1300A) .........................................................14
SUBSTITUTE CHARACTERISTICS OPERATION CONTROL
(FAIL-SAFE ACTION) .........................................................................16
THROTTLE BODIES ...........................................................................21
AIR INDUCTION SYSTEM ......................................................................25
INSTALLING THE REED VALVES .....................................................25
ELECTRICAL .................................................................................................26
ELECTRICAL COMPONENTS ...............................................................26
FUEL INJECTION SYSTEM ...................................................................28
CIRCUIT DIAGRAM (FJR1300) ..........................................................28
CIRCUIT DIAGRAM (FJR1300A) .......................................................29
CHECKING THE FUEL PUMP ...........................................................30
FJR1300 WIRING DIAGRAM
FJR1300A WIRING DIAGRAM

–1 –
GEN
INFO
FEATURES
GENERAL INFORMATION
FEATURES
OUTLINE
The main function of a fuel supply system is to provide fuel to the combustion chamber at the opti-
mum air-fuel ratio in accordance with the engine operating conditions and the atmospheric tempera-
ture.
In the conventional carburetor system, the air-fuel ratio of the mixture that is supplied to the com-
bustion chamber is created by the volume of the intake air and the fuel that is metered by the jet that
is used in the respective carburetor.
Despite the same volume of intake air, the fuel volume requirement varies by the engine operating
conditions, such as acceleration, deceleration, or operating under a heavy load. Carburetors that
meter the fuel through the use of jets have been provided with various auxiliary devices, so that an
optimum air-fuel ratio can be achieved to accommodate the constant changes in the operating con-
ditions of the engine.
As the requirements for the engine to deliver more performance and cleaner exhaust gases
increase, it becomes necessary to control the air-fuel ratio in a more precise and finely tuned man-
ner. To accommodate this need, this model has adopted an electronically controlled fuel injection
(FI) system, in place of the conventional carburetor system. This system can achieve an optimum
air-fuel ratio required by the engine at all times by using a microprocessor that regulates the fuel
injection volume according to the engine operating conditions detected by various sensors.
The adoption of the FI system has resulted in a highly precise fuel supply, improved engine
response, better fuel economy, and reduced exhaust emissions. Furthermore, the air induction sys-
tem (AI system) has been placed under computer control together with the FI system in order to
realize cleaner exhaust gases.
1Ignition coil
2Air filter case
3Intake air tempera-
ture sensor
4Fuel delivery hose
5Fuel tank
6Fuel pump
7Intake air pressure
sensor
8Throttle position sensor
9Fuel injector
0O2sensor
ACatalytic converter
BCrankshaft position
sensor
CCoolant temperature
sensor
DSpark plug
ECylinder identifica-
tion sensor
FBattery
GECU
HFuel injection system
relay
IEngine trouble warn-
ing light
JLean angle cut-off
switch
KAir cut-off valve
6
8
4523GH
J
7
A
90
B
D
C
K
1
IF
E

–2 –
GEN
INFO
FEATURES
FI SYSTEM
The fuel pump delivers fuel to the injector via the fuel filter. The fuel pump maintains the fuel pres-
sure that is applied to the injector at only 324 kPa (3.24 kg/cm2, 46.08 psi). Accordingly, when the
energizing signal from the ECU energizes the injector, the fuel passage opens, causing the fuel to
be injected into the intake manifold only during the time the passage remains open. Therefore, the
longer the length of time the injector is energized (injection duration), the greater the volume of fuel
that is supplied. Conversely, the shorter the length of time the injector is energized (injection dura-
tion), the lesser the volume of fuel that is supplied.
The injection duration and the injection timing are controlled by the ECU. Signals that are input from
the throttle position sensor, crankshaft position sensor, intake air pressure sensor, intake air tem-
perature sensor, coolant temperature sensor, and O2sensor enable the ECU to determine the
injection duration. The injection timing is determined through the signals from the crankshaft posi-
tion sensor and the cylinder identification sensor. As a result, the volume of fuel that is required by
the engine can be supplied at all times in accordance with the driving conditions.
1Fuel pump
2Fuel injector
3Throttle body
4Intake air temperature
sensor
5Throttle position sen-
sor
6Intake air pressure
sensor
7ECU
8Coolant temperature
sensor
9O2sensor
0Cylinder identification
sensor
ACrankshaft position
sensor
ÈFuel system
ÉControl system
Illustration is for reference only.
#4 #3 #2 #1 1
57
4
6
3
A
8
2
0
9
È
É

–3 –
SPEC
SPECIFICATIONS
GENERAL SPECIFICATIONS
ENGINE SPECIFICATIONS
Item Standard Limit
Model code FJR1300: 5JWG (for Europe)
5JWH (for F)
5JWJ (for Oceania)
FJR1300A: 5VS7 (for Europe)
5VS8 (for F)
5VS9 (for Oceania)
----
----
----
----
----
----
Item Standard Limit
Fuel pump
Pump type Electric ----
Model (manufacturer) 5JW 21 (DENSO) ----
Maximum consumption amperage 6.0 A ----
Output pressure 324 kPa (3.24 kg/cm2,46.08 psi) ----
Throttle bodies
Model (manufacturer) ×quantity 42EHS (MIKUNI) ×4 ----
Intake vacuum pressure 33.3 kPa (250 mmHg, 9.8 inHg) ----
Throttle cable free play (at the flange
of the throttle grip)
3 ~ 5 mm (0.12 ~ 0.20 in) ----
ID mark 5JW1 50 ----
Fuel injectors
Model INP-151 ----
Manufacturer NIPPON INJECTOR ----
Quantity 4 ----
GENERAL SPECIFICATIONS/
ENGINE SPECIFICATIONS

–4 –
SPEC
ELECTRICAL SPECIFICATIONS
ELECTRICAL SPECIFICATIONS
Item Standard Limit
Ignition system
Ignition system type Transistorized coil ignition (digital) ----
Ignition timing 5°BTDC at 1,050 r/min ----
Advancer type Electric ----
Pickup coil resistance/color 420.8 ~ 569.3 Ω/Gy–B ----
Transistorized coil ignition unit model
(manufacturer)
F8T818 (MITSUBISHI)
F8T819 (MITSUBISHI) (for F)
----
----
Starting circuit cut-off relay
Model (manufacturer) G8R-30Y-R (OMRON) ----
Coil resistance 180 Ω----
Fuel injection system relay
Model (manufacturer) G8R-30Y-R (OMRON) ----

–5 –
CHK
ADJ
INTRODUCTION/
PERIODIC MAINTENANCE AND LUBRICATION CHART
EAS00036
PERIODIC CHECKS AND ADJUSTMENTS
INTRODUCTION
This chapter includes all information necessary to perform recommended checks and adjustments.
If followed, these preventive maintenance procedures will ensure more reliable vehicle operation, a
longer service life and reduce the need for costly overhaul work. This information applies to vehicles
already in service as well as to new vehicles that are being prepared for sale. All service technicians
should be familiar with this entire chapter.
PERIODIC MAINTENANCE AND LUBRICATION CHART
NOTE:
•The annual checks must be performed every year, except if a kilometer-based maintenance
is performed instead.
•From 50,000 km, repeat the maintenance intervals starting from 10,000 km.
•Items marked with an asterisk should be performed by a Yamaha dealer as they require special
tools, data and technical skills.
No. ITEM CHECK OR MAINTENANCE JOB ODOMETER READING (×1,000 km) ANNUAL
CHECK
1 10203040
1 * Fuel line •Check fuel hoses for cracks or damage. √√√√ √
2 * Spark plugs
•Check condition.
•Clean and regap. √√
•Replace. √√
3 * Valves •Check valve clearance.
•Adjust. Every 40,000 km
4 Air filter element •Clean. √√
•Replace. √√
5*Clutch •Check operation, fluid level and vehicle for fluid
leakage. √√√√√
6 * Front brake
•Check operation, fluid level and vehicle for fluid
leakage. √√√√√ √
•Replace brake pads. Whenever worn to the limit
7 * Rear brake
•Check operation, fluid level and vehicle for fluid
leakage. √√√√√ √
•Replace brake pads. Whenever worn to the limit
8 * Brake hoses •Check for cracks or damage. √√√√ √
•Replace. Every 4 years
9 * Wheels •Check runout and for damage. √√√√
10 * Tires
•Check tread depth and for damage.
•Replace if necessary.
•Check air pressure.
•Correct if necessary.
√√√√ √
11 * Wheel bearings •Check bearing for looseness or damage. √√√√
12 * Swingarm •Check operation and for excessive play. √√√√
•Lubricate with lithium-soap-based grease. Every 50,000 km
13 * Steering bearings •Check bearing play and steering for roughness. √√√√√
•Lubricate with lithium-soap-based grease. Every 20,000 km
14 * Chassis fasteners •Make sure that all nuts, bolts and screws are
properly tightened. √√√√ √

–6 –
CHK
ADJ
PERIODIC MAINTENANCE AND LUBRICATION CHART
NOTE:
•The air filter needs more frequent service if you are riding in unusually wet or dusty areas.
•Hydraulic brake and clutch service
•Regularly check and, if necessary, correct the brake and clutch fluid levels.
•Every two years replace the internal components of the brake master cylinders and calipers as
well as the clutch master and release cylinders, and change the brake and clutch fluids.
•Replace the brake and clutch hoses every four years and if cracked or damaged.
15 Sidestand, center-
stand
•Check operation.
•Lubricate. √√√√ √
16 * Sidestand switch •Check operation. √√√√√ √
17 * Front fork •Check operation and for oil leakage. √√√√
18 * Shock absorber
assembly
•Check operation and shock absorber for oil leak-
age. √√√√
19 *
Rear suspension
relay arm and con-
necting arm pivot-
ing points
•Check operation. √√√√
•Lubricate with lithium-soap-based grease. √√
20 * Electronic fuel
injection •Adjust engine idling speed and synchronization. √√√√√ √
21 Engine oil •Change.
•Check oil level and vehicle for oil leakage. √√√√√ √
22 Engine oil filter
cartridge •Replace. √√√
23 * Cooling system
•Check coolant level and vehicle for coolant leak-
age. √√√√ √
•Change. Every 3 years
24 Final gear oil •Check oil level and vehicle for oil leakage.
•Change. √√√√√
25 * Front and rear
brake switches •Check operation. √√√√√ √
26 Moving parts and
cables •Lubricate. √√√√ √
27 * Throttle grip hous-
ing and cable
•Check operation and free play.
•Adjust the throttle cable free play if necessary.
•Lubricate the throttle grip housing and cable.
√√√√ √
28 * Muffler and
exhaust pipe •Check the screw clamp for looseness. √√√√√
29 * Lights, signals and
switches
•Check operation.
•Adjust headlight beam. √√√√√ √
No. ITEM CHECK OR MAINTENANCE JOB ODOMETER READING (×1,000 km) ANNUAL
CHECK
1 10203040

–7 –
CHK
ADJ
SEATS AND FUEL TANK
SEATS AND FUEL TANK
EAS00040
FUEL TANK
Order Job/Part Q’ty Remarks
Removing the fuel tank Remove the parts in the order listed.
Rider seat Refer to “SEATS AND FUEL TANK”in
chapter 3. (Manual No.: 5JW1-AE1)
Fuel Drain.
1 Fuel tank side panel (left and right) 1/1
2Bolt 2
3Nut 1
4 Fuel sender coupler 1
5 Fuel pump coupler 1
6 Fuel tank overflow hose 1
7 Fuel tank breather hose 1
8 Hose holder 1
9 Fuel hose holder 1

–8 –
CHK
ADJ
SEATS AND FUEL TANK
Order Job/Part Q’ty Remarks
10 Fuel hose 1 Refer to “REMOVING THE FUEL TANK”.
Refer to “INSTALLING THE FUEL
HOSE”in chapter 3. (Manual No.: 5JW1-
AE1)
11 Bolt 1
12 Fuel tank 1 Refer to “REMOVING THE FUEL TANK”.
For installation, reverse the removal
procedure.

–9 –
CHK
ADJ
REMOVING THE FUEL TANK
1. Remove the fuel in the fuel tank through the
fuel tank filler hole with a pump.
2. Remove:
•fuel hose
CAUTION:
Although the fuel has been removed from
the fuel tank, be careful when removing the
fuel hose since there may be fuel remaining
in it.
NOTE:
•To remove the fuel hose from the fuel injec-
tion pipe, slide the cover aon the end of the
hose in the direction of the arrow shown, and
then remove the hose.
•Before removing the hose, place a few rags
in the area under the hose.
3. Remove:
•fuel tank
NOTE:
Do not set the fuel tank down on the installa-
tion surface of the fuel pump. Be sure to lean
the fuel tank up against a wall, etc., in an
upright position.
a
SEATS AND FUEL TANK

–10 –
CHK
ADJ
EAS00043
AIR FILTER CASE
Order Job/Part Q’ty Remarks
Removing the air filter case Remove the parts in the order listed.
Seats Refer to “SEATS AND FUEL TANK”in
chapter 3. (Manual No.: 5JW1-AE1)
Fuel tank Refer to “SEATS AND FUEL TANK”.
Side covers (left and right) Refer to “COWLINGS AND COVERS”.
(Manual No.: 5JW1-AE2)
1 Air shroud 1
2 Air filter case cover 1
3 Air filter element 1
4Tray 1
5 Fuel tank bracket 1
6 Plastic locking tie 1
7 Intake air temperature sensor coupler 1
8 Bypass air unit inlet hose 1 Disconnect.
9 Crankcase breather hose 1 Disconnect.
AIR FILTER CASE

–11 –
CHK
ADJ
Order Job/Part Q’ty Remarks
10 Air induction system hose 5 1 Disconnect.
11 Clamp screw 4 Loosen.
12 Air filter case 1
13 Air filter case breather hose 1
For installation, reverse the removal
procedure.
AIR FILTER CASE

–12 –
FI
FUEL INJECTION SYSTEM
FUEL INJECTION SYSTEM
FUEL INJECTION SYSTEM
1Ignition coil
2Air filter case
3Intake air tempera-
ture sensor
4Fuel delivery hose
5Fuel tank
6Fuel pump
7Intake air pressure
sensor
8Throttle position sensor
9Fuel injector
0O2sensor
ACatalytic converter
BCrankshaft position
sensor
CCoolant temperature
sensor
DSpark plug
ECylinder identifica-
tion sensor
FBattery
GECU
HFuel injection system
relay
IEngine trouble warn-
ing light
JLean angle cut-off
switch
KAir cut-off valve
6
8
4
5
23GH
J
7
A
90
B
D
C
K
1
I
F
E