The FJR has the capability to adjust the overall fuel injector map for each
individual cylinder right from the dashboard. The procedure is
well-documented in the European and Oceanic service manuals, and requires
the use of CO measuring instruments.
But the Yamaha decided to lock out this capability in the bikes they
shipped to North America. It was a conscious decision: they will tell a
dealer how to override the lock-out if the dealer can prove the need, but
it's a big secret from everyone else.
Not any more. This will explain how you can Europeanize (is that a word?)
your FJR so you can have it properly serviced at any shop. Or even at home
if you have the proper equipment. All you have to do is move one little
wire: the Barbarian Jumper (named after the nickname of the fellow who
discovered it.)

First, remove the seat and two left sidecovers. As
with the dash panels, Yamaha used a variety of fasteners on this job,
including Allen head fasteners, push-pin fasteners, and 1/4 turn Philips
head fasteners. See your owner's manual for a more complete description of
removing each. Don't forget the two underneath the sidecover.

Next, remove the airbox cover. At least all 4 of these are the same 1/4
turn fastener. Unfortunately, the one indicated by the screwdriver is
recessed and a PITA.

With the covers out of the way, the ECU is now accessible. Squeeze the
black latch on the top of the connector as you pull it out of the ECU.

On the underside of the connector are 3 white bars. Using a fingernail or
small screwdriver, push the left one (as pictured) in about 1/32". This
unlocks the wires in the connector.

Pin #27 is the 5th from the left on the bottom row. It houses a yellow
wire with a red stripe -- 1/2 of the Barbarian Jumper. Carefully remove
this wire from the connector. Make sure you have the wire for pin 27 --
the other half of the jumper is only 2 pins away at 29, and we want to
leave that half there.
Do not pull on wires -- if they are pulled even slightly out you will not
be able to re-lock the connector. Also, the metal terminal ends are very
fragile and difficult to replace if you separate the wire from the
terminal. Push the wire out gently as shown in the next picture."

Using a small piece of stiff wire (I used some .030 MIG wire, but a
paperclip or safety pin would probably work) gently push up from the ECU
side of the connector to lift the wire to pin 27 and the white plug in pin
25. Do not force anything! The metal terminal ends on the wires are fragile
and easily damaged. Lift the pin out with tweezers or needlenose pliers.

The plug is small. Very small. And bouncy. It can travel a surprising
distance when deflected off the airbox. If you drop it you are in for more
fun than a snipe hunt. Do not ask me how I know this. Use tweezers.

Put the plug in pin 27. Put the wire you removed in pin 25. Make sure they
are fully seated and then re-lock the connector by pressing the left hand
(as pictured) white bar on the top of the connector down until flush (about
1/32") It does not take a lot of force, so if it doesn't want to go you
probably have a wire pulled slightly out. Make sure all the wires in the
left 1/3 of the connector are fully seated and try again.

When you are all done, insert the connector into the ECU until the latch
clicks. If you did it right, it should look like this now.
Your FJR1300 is now ready for you to tackle the
CO Adjustment procedure,
documented here also.
Note: No ECUs were harmed in the making of this web page.
Before attempting this mod there was a great deal of discussion
and analysis
(on the FJROwners online forum)
of the comparative wiring diagrams and possible operating
parameters of the unit. Then the signal levels of the various ECU pins were
sampled with a high impedance probe and oscilloscope to clarify any
ambiguities.
I may be curious, but I ain't stupid.
Nonetheless: all the standard disclaimers apply: Do this at your own risk.
I am not responsible if you let the smoke out of your ECU. YMMV. Etc.
-- Torch.