Yamaha 2006 FJR1300AS User manual

2006
SUPPLEMENTARY
SERVICE MANUAL
FJR1300AS(V)
3P6-28197-E1

ET2D21027
FOREWORD
This Supplementary Service Manual has been prepared to introduce new service and data for the
FJR1300AS(V). For complete service information procedures it is necessary to use this Supplementary
Service Manual together with the following manual.
FJR1300A(V) SERVICE MANUAL: 3P6-28197-E0
EAS20040
FJR1300AS(V) 2006
SUPPLEMENTARY SERVICE MANUAL
©2006 by Yamaha Motor Co., Ltd.
First edition, February 2006
All rights reserved.
Any reproduction or unauthorized use
without the written permission of
Yamaha Motor Co., Ltd.
is expressly prohibited.

EAS20070
NOTICE
This manual was produced by the Yamaha Motor Company, Ltd. primarily for use by Yamaha dealers
and their qualified mechanics. It is not possible to include all the knowledge of a mechanic in one man-
ual. 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 vehi-
cle unsafe and unfit for use.
Yamaha Motor Company, Ltd. is continually striving to improve all of its models. Modifications and sig-
nificant changes in specifications or procedures will be forwarded to all authorized Yamaha dealers and
will appear in future editions of this manual where applicable.
NOTE:
Designs and specifications are subject to change without notice.
EAS20080
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 vehicle operator, a bystander or a person checking or repairing the ve-
hicle.
A CAUTION indicates special precautions that must be taken to avoid dam-
age to the vehicle.
A NOTE provides key information to make procedures easier or clearer.
WARNING
CAUTION:
NOTE:

EAS20090
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.
• The manual is divided into chapters and each chapter is divided into sections. The current section title
“1” is shown at the top of each page.
• Sub-section titles “2” appear in smaller print than the section title.
• To help identify parts and clarify procedure steps, there are exploded diagrams “3” at the start of each
removal and disassembly section.
• Numbers “4” are given in the order of the jobs in the exploded diagram. A number indicates a disas-
sembly step.
• Symbols “5” indicate parts to be lubricated or replaced.
Refer to “SYMBOLS”.
• A job instruction chart “6” accompanies the exploded diagram, providing the order of jobs, names of
parts, notes in jobs, etc.
• Jobs “7” requiring more information (such as special tools and technical data) are described sequen-
tially.
3
4
5
6
1
2
7

EAS20100
SYMBOLS
The following symbols are used in this manual
for easier understanding.
NOTE:
The following symbols are not relevant to every
vehicle.
GM
E
BLS M
91011
12 13 14
15 16
LT New
T
R
.
.
123
456
78
1. Serviceable with engine mounted
2. Filling fluid
3. Lubricant
4. Special tool
5. Tightening torque
6. Wear limit, clearance
7. Engine speed
8. Electrical data
9. Engine oil
10.Gear oil
11.Molybdenum-disulfide oil
12.Wheel-bearing grease
13. Lithium-soap-based grease
14.Molybdenum-disulfide grease
15.Apply locking agent (LOCTITE®)
16. Replace the part

EAS20110 CONTENTS
FEATURES......................................................................................................... 1
OUTLINE OF THE YCC-S (Yamaha Chip Controlled-Shift) SYSTEM......... 1
SPECIAL TOOLS ............................................................................................... 4
GENERAL SPECIFICATIONS ........................................................................... 6
ENGINE SPECIFICATIONS ............................................................................... 7
CHASSIS SPECIFICATIONS ............................................................................. 8
ELECTRICAL SPECIFICATIONS ...................................................................... 9
TIGHTENING TORQUES ................................................................................. 10
ENGINE TIGHTENING TORQUES............................................................ 10
CHASSIS TIGHTENING TORQUES.......................................................... 11
CABLE ROUTING ............................................................................................ 13
PERIODIC MAINTENANCE ............................................................................. 29
INTRODUCTION ........................................................................................ 29
PERIODIC MAINTENANCE AND LUBRICATION CHART........................ 29
ENGINE ............................................................................................................ 31
CHECKING THE CLUTCH FLUID LEVEL ................................................. 31
BLEEDING THE HYDRAULIC CLUTCH SYSTEM .................................... 31
CHECKING THE VEHICLE AFTER BLEEDING THE HYDRAULIC
CLUTCH SYSTEM .................................................................................... 33
CLEANING THE AIR FILTER ELEMENT................................................... 34
CHASSIS .......................................................................................................... 35
ADJUSTING THE SHIFT PEDAL............................................................... 35
ELECTRICAL SYSTEM.................................................................................... 36
REPLACING THE HEADLIGHT BULBS .................................................... 36
GENERAL CHASSIS........................................................................................ 37
HANDLEBARS................................................................................................. 41
INSTALLING THE HANDLEBARS ............................................................. 43

SHAFT DRIVE .................................................................................................. 46
INSTALLING THE DRIVE SHAFT AND FINAL DRIVE ASSEMBLY ......... 46
ENGINE REMOVAL ......................................................................................... 47
REMOVING THE GEAR POSITION SENSOR .......................................... 49
REMOVING THE ENGINE ......................................................................... 49
INSTALLING THE GEAR POSITION SENSOR......................................... 49
ADJUSTING THE GEAR POSITION SENSOR ......................................... 50
CLUTCH ........................................................................................................... 51
BREAKING IN THE FRICTION PLATES AFTER REPLACEMENT........... 55
REPLACING THE CLUTCH MASTER CYLINDER.................................... 55
INSTALLING THE CLUTCH ACTUATOR .................................................. 56
SHIFT ACTUATOR AND SHIFT ROD ............................................................. 57
REMOVING THE SHIFT ACTUATOR........................................................ 59
CHECKING THE SHIFT ROD .................................................................... 59
INSTALLING THE FOOT SHIFT SWITCH................................................. 59
ADJUSTING THE FOOT SHIFT SWITCH ................................................. 60
INSTALLING THE LEFT FOOTREST ASSEMBLY.................................... 61
INSTALLING THE SHIFT ACTUATOR ...................................................... 61
SHIFT SHAFT................................................................................................... 63
INSTALLING THE SHIFT SHAFT .............................................................. 63
MIDDLE GEAR................................................................................................. 64
CRANKCASE ................................................................................................... 66
TRANSMISSION............................................................................................... 68
ELECTRIC STARTING SYSTEM ..................................................................... 71
CIRCUIT DIAGRAM (1/2)........................................................................... 71
CIRCUIT DIAGRAM (2/2)........................................................................... 73
STARTING CIRCUIT CUT-OFF SYSTEM OPERATION ........................... 75
TROUBLESHOOTING ............................................................................... 76
GRIP WARMER SYSTEM................................................................................ 79
CIRCUIT DIAGRAM (1/2)........................................................................... 79
CIRCUIT DIAGRAM (2/2)........................................................................... 81
TROUBLESHOOTING ............................................................................... 83

YCC-S (Yamaha Chip Controlled-Shift) SYSTEM......................................... 85
CIRCUIT DIAGRAM (1/2)........................................................................... 85
CIRCUIT DIAGRAM (2/2)........................................................................... 87
TROUBLESHOOTING ............................................................................... 89
MAINTENANCE OF THE MCU .................................................................. 90
MCU (motor control unit) SELF-DIAGNOSTIC FUNCTION ....................... 90
SELF-DIAGNOSTIC FUNCTION TABLE ................................................... 91
TROUBLESHOOTING METHOD............................................................... 94
DIAGNOSTIC MODE ................................................................................. 95
TROUBLESHOOTING DETAILS ............................................................... 99
ELECTRICAL COMPONENTS....................................................................... 123
CHECKING THE SWITCHES .................................................................. 127
CHECKING THE RELAYS ....................................................................... 130
CHECKING THE YCC-S SPEED SENSOR............................................. 132
CHECKING THE GEAR POSITION SENSOR......................................... 132
CHECKING THE FOOT SHIFT SWITCH................................................. 133
CHECKING THE GRIP WARMERS......................................................... 133
CHECKING THE GRIP WARMER CONTROL UNIT ............................... 134
CHECKING THE DIODE 2 ....................................................................... 134
FJR1300AS(V) 2006 WIRING DIAGRAM

FEATURES
– 1 –
EAS20170
FEATURES
ET2D21013
OUTLINE OF THE YCC-S (Yamaha Chip Controlled-Shift) SYSTEM
Concept
YCC-S offers more enjoyable and easy riding by eliminating the need for the user to operate the clutch,
which also reduces fatigue during long touring.
YCC-S is not an automatic transmission, although it allows the user to shift gears by foot or hand ac-
cording to preference.
When shifting, a signal is sent to the MCU (motor control unit), which ensures optimum clutch operation,
shifting, and engine control. Therefore, the user never needs to operate the clutch, which in turn, reduc-
es fatigue and allows the user to concentrate while riding.
When stopping at traffic lights or in traffic jams, YCC-S operates the clutch instead of the user.
Basic function
To shift gears after starting the engine, the user must use the shift pedal. However, depending on the
user’s preference, the transmission can be shifted by hand after setting the hand shift select button to
“ON”.
When the engine is started, the MCU disengages the clutch. A signal is sent to the MCU when the trans-
mission is shifted from neutral to 1st gear by hand or foot. When the throttle is opened, the MCU then
engages the clutch according to engine r/min. Clutch engagement is controlled optimally by the MCU.
Clutch engagement is not constant in order to provide smooth shifting according to engine require-
ments and conditions.
The YCC-S system will not shift up if the engine r/min is lower than a specified value. Even if the user
shifts up, if the specified value is not met (engine r/min is too low), the YCC-S system will not shift up
until the above-mentioned specified value is met.
Likewise, the YCC-S system will not shift down if the specified value is not met (engine r/min is too
high).
In this case, the throttle must be closed so that the MCU can disengage the clutch until the specified
value is met to prevent the engine from stopping. During this period, a coasting condition will be felt.
The user must shift down properly in order for the YCC-S system to provide a smooth stopping condi-
tion.
The YCC-S system is constantly performing a self-diagnosis when the engine is running. If any trouble
is detected, the MCU automatically stops the YCC-S system and shifting is impossible.

FEATURES
–2 –
Shift pattern
This vehicle is equipped with a constant-mesh 5-speed transmission. The gears can be shifted using
either the shift pedal “1”or the hand shift switch “2”. The hand shift switch has to be enabled by pressing
the hand shift select button “3”prior to being used. The gear positions are shown in the illustration.
1
2
34
5
679
11
12
8
10
1. YCC-S test coupler
2. YCC-S control relay
3. YCC-S indicator and warning light
4. YCC-S motor control fuse
5. Hand shift switch
6. Gear position sensor
7. Neutral switch
8. MCU (motor control unit)
9. Shift actuator
10. Clutch actuator
11.Foot shift switch
12.YCC-S speed sensor

FEATURES
–3 –
Attention
•Do not turn the main switch to “OFF”while the vehicle is moving, otherwise the electrical systems will
be switched off, including the YCC-S system, which may result in loss of control or an accident. Make
sure that the vehicle is stopped before turning the main switch to “OFF”.
•The clutch will be engaged for a few seconds after the engine is stopped using the main switch if the
transmission is not in neutral. This means that the vehicle cannot be moved by pushing or pulling it.
To move the vehicle, turn the main switch to “ON”, and then apply the front or rear brake to disengage
the clutch. A click will be heard when the clutch is disengaged.
•Always stop the engine and turn the main switch to “LOCK”when parking the vehicle.
YCC-S indicator and warning light
•The YCC-S system is constantly performing a self-diagnosis.
•The YCC-S system also performs a self-diagnosis when the main switch is turned to “ON”. The YCC-
S indicator and warning light “1”come on during this self-diagnosis. After the self-diagnosis is com-
pleted, if there were no problems found, the YCC-S indicator and warning light will go off.
•If the YCC-S indicator and warning light come on while riding, stop the vehicle, park it in a safe place,
and then contact a Yamaha dealer.
Because the YCC-S system stops automatically when the YCC-S indicator and warning light come
on, it is impossible to shift since clutch operation is stopped. To move the vehicle, turn the main switch
to “OFF”and place the vehicle on the centerstand. While rotating the rear wheel, push the shift rod
forward and shift the transmission into neutral.

SPECIAL TOOLS
–4 –
EAS20260
SPECIAL TOOLS
The following special tools are necessary for complete and accurate tune-up and assembly. Use only
the appropriate special tools as this will help prevent damage caused by the use of inappropriate tools
or improvised techniques. Special tools, part numbers or both may differ depending on the country.
When placing an order, refer to the list provided below to avoid any mistakes.
NOTE:
•For U.S.A. and Canada, use part number starting with “YM-”, “YU-”, or “ACC-”.
•For others, use part number starting with “90890-”.
Tool name/Tool No. Illustration Reference
pages
Vacuum/pressure pump gauge set
90890-06756
Mityvac brake bleeding tool
YS-42423
32
Magnet base B
90890-06844
Magnetic base stand
YU-A8438
33
Dial gauge & stand set
90890-01252
33
Fork seal driver weight
90890-01184
46
Fork seal driver attachment
90890-01186
Replacement 27 mm
YM-A9409-1
46
Oil seal installing tool
90890-01512
46
Pivot shaft wrench
90890-01471
Frame spanner socket
YM-01471
49

SPECIAL TOOLS
–5 –
Pivot shaft wrench adapter
90890-01476
49
Digital circuit tester
90890-03174
Model 88 Multimeter with tachometer
YU-A1927
50, 60
Test coupler adapter
90890-03149
95
Pocket tester
90890-03112
Analog pocket tester
YU-03112-C
129, 130, 132,
133, 134
Tool name/Tool No. Illustration Reference
pages

GENERAL SPECIFICATIONS
–6 –
EAS20280
GENERAL SPECIFICATIONS
Model
Model 2D21(Europe except (B)and(F))(ZA)
2D22(B)(F)
2D23(AUS)
Weight
With oil and fuel 295.0 kg (650 lb)
Maximum load 208 kg (459 lb)

ENGINE SPECIFICATIONS
–7 –
EAS20290
ENGINE SPECIFICATIONS
Clutch
Clutch type Wet, multiple-disc
Clutch release method Hydraulic inner push
Clutch lever free play 1.9–20.7 mm (0.07–0.81 in)
Friction plate thickness 2.90–3.10 mm (0.114–0.122 in)
Wear limit 2.80 mm (0.1102 in)
Plate quantity 9 pcs
Clutch plate thickness 1.90–2.10 mm (0.075–0.083 in)
Plate quantity 8 pcs
Warpage limit 0.10 mm (0.0039 in)
Clutch spring height 6.78 mm (0.27 in)
Minimum height 6.4 mm (0.25 in)
Spring quantity 1 pc
Push rod bending limit 0.370 mm (0.0146 in)
Clutch pressure plate stroke 2.8 mm (0.11 in) or more
Transmission
Transmission type Constant mesh 5-speed
Primary reduction system Spur gear
Primary reduction ratio 75/48 (1.563)
Secondary reduction system Shaft drive
Secondary reduction ratio 35/37 ×21/27 ×33/9 (2.698)
Operation Left foot and left hand operation
Gear ratio
1st 43/17 (2.529)
2nd 39/22 (1.773)
3rd 31/23 (1.348)
4th 28/26 (1.077)
5th 26/28 (0.929)
Main axle runout limit 0.08 mm (0.0032 in)
Drive axle runout limit 0.08 mm (0.0032 in)

CHASSIS SPECIFICATIONS
–8 –
EAS20300
CHASSIS SPECIFICATIONS
Tire air pressure (measured on cold tires)
Loading condition 0–90 kg (0–198 lb)
Front 270 kPa (39 psi) (2.70 kgf/cm²)
Rear 290 kPa (42 psi) (2.90 kgf/cm²)
Loading condition 90–208 kg (198–459 lb)
Front 270 kPa (39 psi) (2.70 kgf/cm²)
Rear 290 kPa (42 psi) (2.90 kgf/cm²)
High-speed riding
Front 270 kPa (39 psi) (2.70 kgf/cm²)
Rear 290 kPa (42 psi) (2.90 kgf/cm²)

ELECTRICAL SPECIFICATIONS
–9 –
EAS20310
ELECTRICAL SPECIFICATIONS
Gear position sensor
Output voltage (at neutral position) 0.71–0.91 V
Resistance 4.0–6.0 kΩ
Foot shift switch
Output voltage 2.4–2.6 V
Resistance 4.0–6.0 kΩ
Grip warmer
Resistance 1.21–1.48 Ωat 20 °C (68 °F)
Fuses
Main fuse 50.0 A
Headlight fuse 25.0 A
Signaling system fuse 15.0 A
Ignition fuse 10.0 A
Radiator fan fuse 15.0 A ×2
Auxiliary DC jack fuse 3.0 A
Hazard fuse 10.0 A
Fuel injection system fuse 15.0 A
ABS motor fuse 30.0 A
ABS control unit fuse 10.0 A
YCC-S motor control fuse 30.0 A
Backup fuse 10.0 A
Reserve fuse 30.0 A
Reserve fuse 25.0 A
Reserve fuse 15.0 A
Reserve fuse 10.0 A
Reserve fuse 3.0 A

TIGHTENING TORQUES
–10 –
EAS20320
TIGHTENING TORQUES
EAS20340
ENGINE TIGHTENING TORQUES
Item Thread
size Q’ty Tightening torque Remarks
Clutch fluid reservoir bolt M6 1 7 Nm (0.7 m·kg, 5.1 ft·lb)
Clutch actuator bracket bolt M8 2 19 Nm (1.9 m·kg, 13 ft·lb)
Clutch actuator bracket bolt M6 3 10 Nm (1.0 m·kg, 7.2 ft·lb)
Gear position sensor cover M6 2 10 Nm (1.0 m·kg, 7.2 ft·lb)
Gear position sensor screw M5 2 4 Nm (0.4 m·kg, 2.9 ft·lb)
Gear position sensor bracket M5 2 9 Nm (0.9 m·kg, 6.5 ft·lb)
Shift actuator front bolt M8 1 20 Nm (2.0 m·kg, 14 ft·lb)
Shift actuator rear bolt M8 1 20 Nm (2.0 m·kg, 14 ft·lb)
Shift rod bolt M6 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
Shift rod bolt M8 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
Shift rod front locknut M6 1 7 Nm (0.7 m·kg, 5.1 ft·lb)
Shift rod rear locknut M8 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
Foot shift switch screw M5 2 4 Nm (0.4 m·kg, 2.9 ft·lb)
Front shift arm bolt M6 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
Neutral switch M10 1 20 Nm (2.0 m·kg, 14 ft·lb)
YCC-S speed sensor bolt M6 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
LT
LT
LT
LT
LT
LT

TIGHTENING TORQUES
–11 –
EAS20350
CHASSIS TIGHTENING TORQUES
Item Thread
size Q’ty Tightening torque Remarks
Shift pedal bolt M6 1 7 Nm (0.7 m·kg, 5.1 ft·lb)
Shift pedal pivot bolt M8 1 16 Nm (1.6 m·kg, 11 ft·lb)
Pivot shaft locknut retainer bolt M6 1 10 Nm (1.0 m·kg, 7.2 ft·lb)
LT
LT
LT