
2006-09 Yamaha R6S
PARTS LIST
Installation Instructions
1Juice Box Pro
TM
1 USB Cable
1 Top Tune CD-ROM
1 Installation Guide
2Velcro
1 Alcohol swab
FOR RACE USE ONLY
DOWNLOAD THE TOPTUNE SOFTWARE
AND LATEST MAPS FROM OUR
WEBSITE:
www.twobros.com
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PLEASE READ ALL DIRECTIONS BEFORE STARTING INSTALLATION
401 S. Grand Ave. Santa Ana, CA 92705
(800) 211-2767 www.twobros.com
2006-09 Yamaha R6S - 1

Selecting the Map Position
The Juice Box Pro comes loaded with up to ten maps. Using a #1 Phillips
screwdriver, turn the map select dial to toggle between the loaded maps. Refer to
the map position table below for the maps included in your Juice Box Pro.
Using the RPM Range Dials
The Low, Mid, and High RPM Dials refer to the RPM range, in thirds, of your
vehicle. Each dial allows +/- 10% fuel adjustment on top of what fuel changes are
done in the map. With the dial facing straight up, there is no additional fuel change.
For example, if your vehicle revs to 15,000 RPM:
• the low RPM dial will adjust 0-5000 RPM
• the mid RPM dial will adjust 5001-10000 RPM
• the high RPM dial will adjust 10001-15000 RPM
Using Top Tune
Take your tuning to the next level with the Top Tune software.
Position 0 Zero map
Position 1 Stock exhaust
Stock or aftermarket air filter
Position 2 Two Brothers slip-on exhaust
Stock or aftermarket air filter
USB Port
High RPM Dial
Mid Dial RPM
Low Dial RPM
Map Select
Status Light
(Power to Unit)
2006-2009
Yama h a R 6S
2006-2009
Yama h a R 6S
Installing the To p Tune Software
1 Insert the CD provided into your computer’s cd-rom drive. The launch program
will run automatically.
If auto-run is disabled, double-click the My Computer icon then double-click the
CD drive icon. Double-click TBR Top Tune.exe to manually start the CD.
2 Click Install Software and follow the on-screen instructions to install the Top
Tune software. The Top Tune software and maps will be stored in C:\Program
Files\TBR Top Tune.
3 Click Map Database. All maps will automatically be installed to the C:\Program
Files\TBR Top Tune\maps folder.
Loading Additional Maps
1 Connect the USB cable from the computer to the Juice Box Pro. Verify the cable
is fully seated in the Juice Box Pro.
2 Run the Top Tune software by double-clicking the program icon installed on your
desktop or on your start menu.
3 Click Open Map File and select a map file.
4 Click Send Map. You can send the map to any of the ten map positions.
Altering Maps Using Top Tune
The values in the map represent a percentage of fuel change over stock. A value of
10 in the map indicates at that throttle position and RPM range the vehicle will be
10% richer than stock. If the value is -10, then it would be 10% leaner than stock. You
have the ability to fine tune your fuel curve by altering these values. The Top Tune
software allows a value of +250 to -100 in each cell.
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2006-09 Yamaha R6S - 2

Figure AFigure BFigure C
Juice Box Pro
harness
Juice Box Pro
harness
Juice Box Pro
harness
ground wire
The ignition must be turned OFF before installation.
1 Remove the main seat and the passenger seat.
2 Prop the front of the fuel tank up.
3 Remove the rubber plug in the tail section near the tool kit.
4 Lay the Juice Box Pro in the tail section.
5 Route the Juice Box Pro harness through the hole and down the right side of the
bike as shown in Figure A.
6 Route the Juice Box Pro harness under the cross member for the subframe as shown
in Figure B.
7 Attach the ground wire from the Juice Box Pro to the negative side of the battery as
shown in Figure B.
unplug
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unplug
8 Unplug the two 6-pin connectors from the throttle bodies as shown in Figure C.
One connector is black and the other connector is clear.
2006-09 Yamaha R6S - 3

9 Attach the connectors from the Juice Box Pro to the stock wiring harness and the
throttle bodies as shown in Figure D.
Attach the colored connectors from the Juice Box Pro to the matching stock
connectors.
Figure DFigure E
10 Using the supplied velcro, secure the Juice Box Pro in the tail section as shown in
Figure E.
Make sure to clean both surfaces with the alcohol swab before attaching.
11 Lower the fuel tank back into place and bolt it down.
12 Reinstall the passenger seat and the main seat.
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2006-09 Yamaha R6S - 4