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Yamaha WR 400 Installation Manual

1. Get a degree in Mechanical and Electrical Engineering. (Just kidding!)

2. Remove the seat, side panels, and gas tank.

If you are color blind or even think you might be a little color blind, now is the time to get
someone to assist you. Successful installation of the kit requires good color recognition. You
want to go riding this weekend, don't you?

3. Unplug the yellow, blue and black taillight wires from the stock wiring harness.

4. Unplug the headlight from the stock wiring harness and remove.

5. Remove the kill switch. Unplug the black/white wire and the black wire from the connectors
that were under the fuel tank.

6. Remove the headlight on/off switch. Unplug the three pin connector from its mate that was
under the fuel tank.

7. Remove the stock AC voltage regulator (Photo 1) found mounted on the left side of the
steering tube. Unplug its connector from the stock wiring harness.

8. This time would be a good time to

perform the stator modification to get
AC Voltage this task out of the way. Refer to the
Regulator color “WR 400 Stator Modification”
sheet enclosed to complete this
portion of the installation.

Photo 1

9. License Plate Mount Installation: Locate the aluminum license plate mount and license
plate light assembly. If you have the alternative DOT taillight/license plate mount go to step
9B. Remove the rear most nut securing the stock taillight assembly (underneath the fender)
(don’t lose the little compression tube and washer). Temporarily install the license plate mount
to this location and mark the fender where it needs to be drilled for the rear mounts. Drill the
fender in two places with a 1/4” drill and reinstall the license plate assembly using the stock
taillight mount and the 6 x 20 mm countersunk screws, bezels and nylock nuts (Photo 2). Run
the wires forward along with the taillight wires and up through the grommet in the fender.

9B. Optional License Plate/DOT

Taillight Installation: Remove the lens
from the stock taillight. Remove the
three nuts holding the gray taillight base
to the fender and remove base. Locate
the 6 x 25 mm bolt supplied with other
taillight mounting hardware (small bag
#3) and a compression tube from the
stock taillight (little brass colored tube
that fits inside rubber grommet.
Temporarily install the license plate
bracket assembly using the rear most
taillight mounting hole to determine the
drill locations of the two rear mounts
(You will have to remove the taillight Photo 3
temporarily to be able to mark the fender). Mark the fender and drill in two places with a 1/4”
drill. Install the license plate hanger to the rear most mounts using the 6 x20 mm countersunk
screws, bezels and nylock nuts. (Photo 3). Make sure to install the taillight ground wire under
the nut for the left hand stud (Photo 4). Run the wires forward and up through the grommet in
the fender.

A plastic cover is supplied to

cover the opening left by the
stock taillight. Transfer drill a
Install ring hole in the fender for mounting
terminal the plastic cover. Install the
under this compression tube provided
nut between the cover and the
Ground bottom of the taillight well.
Photo 4

10. Rear Turn Signal Installation: Turn signal mounting requires that you drill a 3/8 inch hole
in either side of the rear fender near where it meets the side panels. You can achieve a clean,
durable installation using this mounting location.
Mount the rear turn signals by drilling a 3/8 hole in the rear fender in the location shown in
Photo 5, 1-3/4 inches back from the front edge (edge just behind subframe) and 2-1/16 “ up from
the bottom edge.
Important Note: The left rear turn signal leads are two inches shorter than
the right turn signal leads.

Run the left turn signal wires forward along with the taillight wires, up through the grommet in
the fender to the area just behind the airbox crossmember and above the fender. Run the right
turn signal wires forward along the right frame rail, and up to the same location behind the

Photo 6 11. Brake Light

Installation: The WR 400 uses a
hydraulic brake switch. This requires
replacing the rear master cylinder banjo
bolt with a specially made switch.
Installing the switch requires bleeding
the rear brake. If you do not feel
competent bleeding your rear brake, Banjo Bolt
please refer this job to a qualified
mechanic as failure to do it correctly
will make the brake inoperable.

Remove the rear master cylinder guard. Brace

Remove the bolt holding the brake fluid Master
reservoir to provide access to the master cylinder
cylinder. Loosen the banjo bolt securing here
the rear brake line to the master cylinder. Photo 7
Typically, this bolt will be very tight and
loosening it will bend the support hanger for the master cylinder if not supported. Brace the
master cylinder with a wrench or lever as shown in Photo 7.

Brake Fluid
Brake Switch
Remove the banjo bolt and replace with the hydraulic switch. Make sure to install the copper
crush washer from the stock bolt under the switch. Torque the switch assembly to 25 lbf-ft.
Run the brake switch wires up the rear subframe triangle to the area behind the airbox cross-
Bleeding the Brakes: (Do not begin this process unless you have a fresh can of brake fluid)
Re-install the brake fluid reservoir and
remove the lid. Put the box end of 8mm wrench over the brake bleed nipple and install the bleed
hose (supplied) tightly over the nipple. Position
the loop on the hose above the nipple as shown in Photo 9 Keep loop
Photo 9 with the other end of the hose in a
container to catch the fluid. Crack the bleed above
nipple open about 1/8 to a quarter turn keeping the bleed nipple
loop in the hose vertical. Slowly depress the
brake pedal to fill the hose with fluid. Pump 8 mm Wrench
slowly until you have brake fluid extending up Bleed Nipple
into the loop, then you can pump the pedal fairly
aggressively to drive air out of the system - The
fluid above the bleed nipple will prevent air from
re-entering the system. DO NOT LET THE
NEEDED. Pump the pedal until there is no more bubbles, then close the nipple with the wrench.
Double check that the pedal is firm and the brake works properly.

12. Voltage Rectifier/Regulator and Battery Installation: The battery and rectifier/regulator
install inside the airbox on the right hand side. The WR airbox has a double wall for intake noise
isolation and for cosmetic reasons. You will need to remove the right outside wall of the airbox
temporarily to install the battery and voltage regulator. The outer wall is held on with two 1/8”
pop rivets. Drill out the center
of the pop rivets with a 1/8”
Drill out 1/8” drill to remove the pop rivets
pop rivet Right side and remove the cover (See
here inner airbox Photo 10).
Battery Remove the lid to the WR
mounting airbox. You will not need to
bolts reinstall it
Drill out 1/8” Using the template provided at
pop rivet Regulator
the back of this instruction
here mounting
manual, drill the mounting
holes for the battery and
Photo 10
Mount the Baja Designs voltage
rectifier/regulator (aluminum block with green potting) to the front two mounting holes using the
slot head screws provided. The heads of the screws need to be on the outside of the airbox.
The wires of the regulator should be towards the top (See Photos 10 & 11).

Mount the aluminum “L” bracket provided to the two rear most holes in the airbox. Two
washers should install between the bracket and the airbox wall on the inside of the airbox to
allow room for a zip tie to fit around the bracket. Remove the backing from the double sided
tape and install the battery to the “L” bracket with the wires coming out towards the top rear of
the airbox. Secure the zip tie around the battery and bracket. Do not pull the zip tie too tight -
excessive force on the zip tie can separate the spot welded tabs inside the battery.

Reinstall the outside cover of the airbox using the 1/8” pop rivets provided. If you do not have a
pop rivet gun, use the small 4 mm fasteners provide instead.

13. Field Effect Transistor Installation: The "FET" is a small rectangular black box with an
aluminum mounting tab and three wires contained in your parts bag. Its function is to save your
battery from unnecessary current drain when the bike is stalled but the ignition is still on. It
senses AC voltage on the stator output and shuts the headlight circuit off when no voltage is
present. One peculiarity of this circuit is that the horn frequency will sometimes fool the device
when the engine is off, and the headlight will come on when you honk the horn. This is
normal behavior for the system.

Remove the top bolt

securing the ignition coil to
the frame (right hand side of
bike next to carburetor.
Install the FET switch to
this location (Photo 12) FET
using the Allen screw and Ground lead
spacer provided. Make sure
to reinstall the ground lead
between the coil and the Spacer
spacer. Suggest using blue
loctite on this bolt, as this is Run Wires
a critical ground to ignition Behind
function. Coil

Photo 12

14. Turn Signal Switch Installation: Install the turn signal switch on the left handlebar next to
the grip as shown in Photo 13. The clutch perch will have to be moved to the right to make room
for the switch. Run the wires along the backside of the handlebar and down over the front of the
triple clamps.

15. Power Switch Installation:

Mount the switch under the front
left handlebar pinch clamp bolt
(Photo 14) and run the wires
straight down against the triple
clamp and behind the clutch
cable. Run a zip tie around the
odo mount and the power switch
wires to strain relieve the wires.
Note that the window in the
power switch is a high beam
Photo 14 High Beam
16. Horn Installation: Install the horn under the left
hand bolt of the lower headlight mounting bracket as
shown in Photo 15. If you are using the optional
DOT approved halogen headlight, you may remove
this bracket assembly. The horn is pre-mounted in
the headlight shell. Headlight
17. Wiring Harness Installation: Locate the long
multi-conductor cable with the nylon multi-pin
connector at one end. Gently plug this connector
together with the one in the front wiring harness. Do
not force. If you have trouble plugging the two
together, realign the male pins with a small screwdriver
to get a good match. Note that dielectric grease has
been applied to the female terminals to help prevent Horn
corrosion. This grease can be purchased at any Here
automotive parts store.

Multi- conductor
wire routing

Photo 15
Position the multi-pin connector so that it sits just to the left of the steerer tube. With the
handlebars fully turned to the right to make sure there is enough slack in the cable, run the wire
down along the left side of the frame, along the stock wiring harness, along the main frame
backbone (Photo 16), and then along the inside to the left subframe tube to the area behind the

18. Flasher Installation: If using the stock headlight,

install the flasher to the inside of the headlight (on the right Photo 17
hand side) by drilling two 3/16” holes and using a zip tie as
shown in Photo 17. Position the flasher so that the
terminals face down. If using the optional DOT approved
HP headlight, skip to the next step. The flasher should
already be installed to the inside bottom of the headlight.

19. Front Turn Signals:, Loosely mount the front turn

Zip Tie
signals with the brackets provided as shown in Photo 18
using the longer bolts included. Do not mount the headlight

Drill 3/16”
Turn Two Places

bracket 20. Front Wiring Connections: You will now
make all the connections required at the front of
the bike.
Photo 18
A. Ignition Switch: The only place the Baja Designs kit interfaces with the WR’s ignition
system is through the kill button lead. In no other way does this lighting kit effect the operation
of the motorcycle’s ignition system. The lighting system and ignition system are completely
separate of each other. Locate the ignition extension lead (white/black pair of wires about
18” long) in the parts bag. Plug the white female connector into the white male lead that
comes from the Baja Designs power switch
assembly. Plug the black male on that end into Photo 19
the black double female connector in the front This
harness. Run the extension lead back along the connector is
stock wiring harness and connect the white lead not used in
to the black/white lead in the stock harness dual sport kit
(female connector) where the kill switch
connected previously (Photo 19). Connect the
black extension lead to the corresponding male Connect black
black connector in the stock harness. and white
The rocker switch on your handlebar will function
extension leads
as a kill button and power switch for the lighting.
This will prevent you from forgetting to shut off the

lights when you turn off the bike, lessening the chance for a dead battery. Note this switch must
now be on (depressed on the end with the Hi-beam indicator) for the bike to run.

Note: Disconnecting this white lead will completely isolate the Baja Designs wiring harness
from the bike’s stock ignition system, and the bike will run whether or not the switch is on or
the wiring is damaged.

B. Turn Signals: Plug the green and black wires into the right turn signal. Plug the brown and
black wires into the left turn signal

C. Horn: Connect the black and purple pair of wires to the push on terminals at the back of the

D. Headlight and Flasher: Important - If using the stock headlight, replace the
stock bulb with the halogen 35/35 watt high low beam bulb supplied. Do not
touch the glass portion of the bulb with your fingers. If you do, the oils from
your fingers will create a hot spot on the quartz globe and cause the bulb to
fail prematurely.

The stock stator does not have enough power to keep the battery charged and
run the dual sport kit with the stock bulb. If you want to run the brighter 55/60
watt bulb, Baja Designs can rewind the stator to boost its peak output from 80
watts to 130 watts. ($130.00)

Plug the headlight connector (black three prong connector) into the back of the headlight.
Connect the yellow wire to the yellow wire from the switch panel. Connect the black wire to the
black wire from the switch panel (These wires are normally pre-connected). Connect the red
and white wires to the flasher. The red wire goes to the terminal labeled "X" and the white
wire connects to the terminal labeled "L".

Install the headlight. Turn the handlebars from side to side while observing the wires behind the
headlight. Make sure they move freely and do not pull or pinch against the cables or other parts
of the bike.

21. FET and Stator Extension Leads: Locate the red, orange, and double yellow extension
leads from the parts bag. At one end of these wires is a pair of male connectors (one yellow, one
with a white band. Plug these two male connectors into the yellow and white female leads from
the stator as shown in Photo 20. Don’t miss this step, these are the main power supply leads
for your system.
Photo 20 Run the leads back between the upper engine
mounts and above the carb to the area behind
the FET switch (Photo 12). Connect the
orange, red and yellow wires to the
matching wires on the FET. Run the
remaining four wire bundle across to the
left hand side of the bike and along the
Connect Stator
Leads Here
inside of the left sub-frame rail with the gray multi-conductor harness, to the area just behind the

22. Rear Wiring Connections: You will now make all the connections required to the wiring
harness at the rear of the bike. Take your time to do a neat job here so that you will have a
reliable lighting system. Refer to photographs to copy wiring layout. If you make a mistake in
the following steps, the worst that could happen is the bike will catch fire and burn to the ground

Refer to Photo 21 and Photo # 9 of the color stator modification sheet for wire placement
and layout.

A. Run the wires from the voltage regulator towards the back of the airbox and install a zip tie at
the back right corner of the airbox.

B. Plug the black male lead from the rectifier/regulator into the shortest black female lead
from the main wiring harness.





Photo 21
C. Temporarily Remove the fuse from the fuse holder.

D. Plug the short black pigtail off the black voltage regulator lead with the female connector
into the male black lead from the battery.

E. Turn the red male lead from the voltage regulator back on itself and plug it into the red
lead from the battery.

F. Locate the red, orange, and double yellow extension leads from the parts bag. Plug the two
yellow male connectors from the voltage regulator into the twin yellow female connectors
from this extension lead.

G. Locate the orange lead in the stator and FET extension harness, and plug it into the
orange lead from the main gray multi-conductor harness.

H. Plug the red male lead from the extension harness into one side of the red double female
connector from the main gray multi-conductor harness.

I. Plug the female end of the fused lead into the blue lead from the main wiring harness.

J. Run the taillight wires across the back of the subframe cross member and then plug the blue
wire into one of the blue/red female connectors from the main wiring harness.

K. Plug the black taillight wire into the closest black double female connector from the main
wiring harness.

L. Plug one of the wires from the right turn signal into the other side of this black double
female connector.

M. Plug the other lead of the right turn signal into the green lead of the main wiring

N. Locate the red and yellow pair of wires coming up form the brake light switch. Plug the red
wire from the brake light switch into the other red/blue single female connector from the
main wiring harness.

O. Plug the yellow lead from the brake light switch into the yellow lead from the taillight.

P. Plug one of the leads from the left turn signal into the brown wire from the main wiring

Q. Plug the other lead from the left turn signal into the black double female connector that is
on the end of a short pigtail in the main wiring harness.

R. Plug the black lead from the license plate light into the other side of this black double
female connector. (Not Applicable to kits with DOT Taillight

S. Plug the red lead from the license plate light into the open slot in the red double female
connector from the main wiring harness. (Not Applicable to kits with DOT Taillight)

T. Re-install the fuse into its holder.

The wiring installation is now completed!! Depress the power switch to the right (On the side
with the Hi Beam indicator lamp). The rear taillight should come on. Try the turn signal
switch to the right and the left. Both the front and the back signal should alternate on and off.
Honk the horn (unless its after 11 PM!). The headlight will not come on until the engine is
running. Note: On some systems when the engine is off, the headlight will come on when
you honk the horn. This is a peculiarity with the FET headlight switch which senses the
horn frequency and interprets it as the engine running. This will in no way affect the
normal operation of the system.

If every thing is working properly congratulate yourself on a job well done. If not, don't worry,
it's not rocket science and we should be able to figure it out. All the components were checked
for operation prior to being shipped to you so something is probably not connected correctly.
See the trouble shooting list in a later section.

19. Wrapping it Up: It is important

that all the wires be properly routed
and secured. Double check the
photos and sketches with regards to
wire routing. Make sure the wires do
not pass over any sharp edges, are
pulled overly tight, or can be crushed
by the seat, tank, fender, etc. Use all
the zip ties provided to securely
fasten the wires. Any unwanted
movement or chafing means early
failure when off the road. Note :
When zip tying the wires, do so
separately of the radiator vent hoses
to the overflow tank. There should
be no ties around these hoses other
than the ones that were stock on the
bike. Refer to Photo 22 as to how
the wires should be routed and zip
tied at the rear of the bike. Make
sure all the silicone rubber connector
boots and the connectors are pushed
firmly together and no bare metal is
exposed. Put on the seat, tank, and
side panels, slide on down to your
Photo 22 local DMV, and then go roost!


Nothing Happens When You Turn the Power Switch On.
• Fuse is blown. Check for bare wire or terminal shorting against the frame or another wire.
• Multi-pin connector not properly connected.
• Battery connection poor. Make sure the connectors are fully seated.
• Battery is dead. Measure voltage with voltmeter, or connect a 12 volt light across it.
• Poor connection at the blue wire junction and the fuse lead.

The Turn Signals Won't Come On, or Won't Flash

• The wires on the flasher are connected backward. The red wire goes to the terminal labeled
• Check turn signal wire connections.
• Make sure you have connected the correct wires to the turn signals. Check instructions.
• Battery voltage is low. If the battery voltage is low, the turn signals won't flash, or will flash
very slowly. Running the bike will cure this as well as charge the battery.

The Brake Light Won't Come On

•. The rear brake system is not properly bled.
• Maybe it's on already. Brake and tail connections are reversed. The brake light is already on
so their is no increase in light intensity when you activate the brake. Check the yellow and blue
taillight connections.
• Short the two leads together at the brake switch. If the brakelight comes on, either the brake
switch is defective, or the brake system is no properly bled.

Everthing Works Except the Headlight

• The bike has to be running for the headlight to work.
• Make sure the three prong connector is correctly plugged in and that the wires leading to it are
plugged into the harness.
• Does the high beam indicator come on when the bike is running and high beam selected? If
so, the bulb is burned out or defective.
• If none of the above is successful, disconnect the red and orange leads that plug into the FET,
and plug them into each other (not the leads on the FET). This bypasses the FET switch. If the
headlight works now when the power switch is on, then either the FET is defective or one of the
stator leads, stator extension leads or the yellow lead to the FET has a short to ground. Inspect or
measure with an Ohm meter.

If you still need assistance, call Baja Designs at (619) 792-0213.

Care and Feeding of your Battery: Your kit contains a 12 volt 0.8 ampere-hour Ni-Cad
battery. These batteries are very durable, require no maintenance, and can be mounted in any
position. There are certain things you can do however to maximize its life. The alternator and
voltage regulator in your kit keep your battery fully charged while you are riding, however, when
you turn the engine off and the lights are still on the battery is being discharged. With the new
transistor switch it will take about 30 minutes for the taillight to discharge the battery. With the
Ni-Cad battery if you forget and leave the lights on, don’t sweat it. You can deep cycle (drain
down and charge back up) a Ni-Cad all you want.

If you are doing a lot of slow trail riding where you are on the brakes a lot, the battery may
slowly discharge. The WR 400 has a wimpy stator stock (about 80 watts at 5000 rpm), so if you
are doing a lot of slow and go riding, unplug the headlight to charge the battery back up.

Riding the bike will recharge a drained battery (good excuse for riding, huh?) (for best results,
disconnect the headlight temporarily while the battery recharges) or you can recharge it with a
small trickle charger (we do not recommend this unless absolutely necessary). Do not charge it
with more than 0.5 amperes, and keep an eye on the amount of time and charging voltage. When
the voltage across the battery gets up to 14.5 to 14.8 or it feels warm to the touch, disconnect the
charger. Overcharging will kill a battery faster than anything. A battery measuring 12.9 to 13.2
volts when not connected to a load or a battery charger is fully charged.

If the bike is going to be sitting for more than a month, it is recommended that you
disconnect the positive terminal of the battery to prevent it from discharging. There is a
small amount of current that leaks back through the rectifier when it is connected.

Maintenance: Occasionally examine the wires in your lighting system to make sure they are not
chaffing or binding so that they don't cause you a problem when you're out on the trail or on the
road. A well routed, properly secured wiring system is key to getting long life and trouble free
performance from your conversion kit. The light bulbs take a beating on a dirt bike, especially
the rear taillight’s. The continuous vibration and impact can cause the bulb contact to
prematurely oxidize, causing the bulb to fail. Occasionally remove the bulbs (taillight and turn
signals) and scrape the soft contact at the base of the bulb and clean its mating contact in the
lamp assembly.

Service Tips
If you need access to the carb or shock absorber, it is not necessary to unplug any wires except
for the two wires going to the hydraulic brake switch. Simply loosen the top subframe mount,
remove the bottom subframe mounts, unbolt or remove the muffler, loosen the airboot on the
carb, and rotate the subframe up and forward to provide access as shown in Photo 23 (XR 400
shown). We use a tie down to hold it in place. If you need to remove the subframe, do not
unplug all the wires, unplug just the FET wires, the stator leads, the brake light switch and the
large multipin connector at the end of the gray main harness. This will allow you to remove the
entire subframe without disturbing any of your wiring or zip ties.

Baja Designs • 7558 Trade St

San Diego • California • 92121 • (619) 578-9111
Fax (619) 578-9077
E-Mail: bajades@bajadesigns.com
Internet: http://www.bajadesigns.com