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Yamaha FJR Motorcycle Forum

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Remove, clean and lube rear brake pedal with waterproof grease. Same with shifter linkage. Remove, clean and lube front brake and clutch levers. Pay attention to the brass bushing in the clutch lever that pushes the plunger.
At some point, you should look at greasing the bushings in the rear suspension relay arm. Lots of info here.
Check u-joint and drive splines for corrosion and lube.
Check that recalls have been performed. 2006 had some electrical grounding issues. Search "spider" for lots of reading.
Check date codes on tires.

Good luck with the bike and welcome to the forum.

Edit: Be aware of rattling noise on the right side. Some early Gen II FJRs had problems with a weak cam chain tensioner (CCT). I would recommend replacing it at some point. Perhaps along with coolant, sparkplugs and throttle body synchronization (TBS)when you do your first valve check. CCT failure could grenade the engine - not common, but there were a few reported instances.
 
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going to do clutch and brake fluid
In case you weren't aware...
When it comes to bleeding/flushing brakes, do the left front caliper followed by the UPPER BLEEDER on the right front caliper. These from the right reservoir on the handlebars. (Right caliper has TWO bleeder nipples.)
The FJR has a linked braking system and the LOWER BLEEDER on the right front caliper is bled using the rear brake pedal (and reservoir). Do this one before bleeding the rear brake caliper.
Some people love Speed Bleeders to help facilitate bleeding the hydraulic circuits and others love to hate them. I am in the latter category and have never felt the need to replace the original bleeders.
I would do the clean/lube/servicing of the levers and pedals before bleeding...
 
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