Brakes failed

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IMHO, the rear rotor is badly scored and has been badly overheated. I would replace it, even if not warped. Fluid - no question. Thorough flush. Doesn't take much time and almost impossible to screw up, unless you are incompetent. Pads - I would reserve judgement until I saw them, but would most likely change the rear pads.
 
Agree with finding a new shop. I can't believe they didn't change out the rotor and pads.

And there is no special tool needed to flush the ABS module. I'd do a complete flush/bleed. It's not rocket surgery and the process is well documented.
 
Bleeding brakes in a nutshell....

1) Left front caliper
2) Right front top bleeder
3) Rear caliper
4) Right front bottom bleeder
5) Exercise the ABS pump by
a) bike on center stand
b) jumper the light blue and black wires on the connector up under the dash panel near the battery
c) Side stand down, bike in gear (I think)
d) turn on key
e) hold the starter button for 4 seconds
f) pull lever and step on pedal at the same time and hold (you'll feel it cycle/pulsate from lever to pedal to lever again until it stops)
e) turn off key
6) Repeat ABS pump again if you want
7) Repeat steps 3 & 4. Remove jumper wire.
 
Agree with finding a new shop. I can't believe they didn't change out the rotor and pads.

And there is no special tool needed to flush the ABS module. I'd do a complete flush/bleed. It's not rocket surgery and the process is well documented.
Have you lubed the rear brake pedal pivot
I have had it hang up on me two times.
WD-40 to test it out/then remove and grease properly.
 
Have you lubed the rear brake pedal pivot
I have had it hang up on me two times.
WD-40 to test it out/then remove and grease properly.
Already mentioned a couple of times but bears repeating. Removing to clean and lube with waterproof grease should be done (at least) annually. I check mine for smooth operation and "snap" back to home position pretty much any time I go out. Never had a hang up on my FJR, but did on a Yamaha Venture. WD-40 got me home and I fixed it properly.
 
"official" manual method for the rear is bleed front lower first, then rear. However... I wouldn't think it would make a bit of difference. Same with front. The manual says left first, then right upper. So, I do it thinking there is mojo in it....

Activate the ABS: Do not activate any brakes until you apply both at once later....
Install jumper (I use an alligator clip, open it all the way and it will bridge both terminals)
Turn the engine-off button set to off
Turn key on
Press and hold start button at least 4 seconds
Activate ABS pump by engaging both front lever and rear pedal at the same time.
Hold down both until you feel the pump in the lever, in the pedal, and back in the lever
Key off and remove jumper
Re-bleed front lower and rear

The front system and rear system are separate. However, the rear system also activates the front right lower pad at the same time as the rear. Thus, a "linked" braking system. The front system operates both pads on the left and the upper pad on the right.

I would think if you dragged the rear, you also were dragging the front on the right. Not sure it would create enough heat to boil in the front system, but the right lower would create enough heat while the rear was on if it was dragging as well to boil the lower section of that caliper.
 
"Mobile 1 10w-40". I did not know they had "Racing" oil. Now I am not sure if it said "High Mileage" or just 10W-40.
I hope this isn't just restating the obvious, but would not use the automotive-type Mobil-1 that isn't JASO MA/MA2 cert for wet clutches. The AE system can really work the clutch over if the rider insists on being lazy with the downshifts and using the perfectly-controlled slippage for takeoffs in the wrong gear. Automotive oil friction modifiers cause m/c wet clutch plates to get more wear from slower lockup. Not all of the old oil comes out during an oil change, so If I had the wrong oil, I'd change it again in short time and put some high-end m/c racing oil or Rotella T6 which is a great cheaper oil if you change in shorter intervals.
 
I took it for a couple rides and at this point everything is working as usual. I'm convinced I boiled the fluid by resting my foot the rear brake. On the recent rides I made sure the toes were not on the brake.

Thanks for the brake fluid changing instructions. Since things are working I am going to wait until winter and then try to bleed the brakes again. I did it myself a couple years ago but did not know about the ABS module needing special handling. I just hooked up a bottle and pumped until new fluid came out. Not having special tools except a bottle and hose I set up for the outflow, it was a bit of a stop and go process. Since the hose end sat in fluid I did not have any air bubble issues and could watch the level in the reservoirs as I pumped the brakes.

I am disappointed, and kind of surprised, that the shop did not do the brake fluid change. They said they would likely do it given the issue but when I picked up the bike they said the fluid looked really good, plenty of meat left on the pads and they were certain it did not need it. It may be better if I do it myself. I get the feeling they don't see many FJRs. It is a small shop and it appears they are moving away from selling motorcycles and into electric bicycles. I asked and they said it was hard to get motorcycle inventory from Yamaha.
 
I hope this isn't just restating the obvious, but would not use the automotive-type Mobil-1 that isn't JASO MA/MA2 cert for wet clutches. The AE system can really work the clutch over if the rider insists on being lazy with the downshifts and using the perfectly-controlled slippage for takeoffs in the wrong gear. Automotive oil friction modifiers cause m/c wet clutch plates to get more wear from slower lockup. Not all of the old oil comes out during an oil change, so If I had the wrong oil, I'd change it again in short time and put some high-end m/c racing oil or Rotella T6 which is a great cheaper oil if you change in shorter intervals.
I'm going to have to check on the JASO MA/MA2 rating, if I can find the bottle or my order. However, I've been using this for a couple years now. Prior to that I used the Rotella 5 Diesel oil and while that worked I did feel a little more slip. The bike has 32,000 miles on it now and seems a bit smoother than during the first 20,000 miles. :) I thought I read someplace that typical clutch life is 36,000 miles. I am surprised mine still works since I tend to do a lot of engine braking. I really don't push the bike hard but I am really bad at synching the engine speed and gears. I'm one of those people that would buy an automatic, though I don't have problems working the clutch on my 1993 Goldwing (which I don't ride much).

BTW, the AE system is impressive. When I first got the bike I forgot to downshift coming to a stop, then had to accelerate fast. I took me from 0 to 60 all in 5th gear. No, I did not repeat the feat...
 
I thought I read someplace that typical clutch life is 36,000 miles.
Typical FJR clutch lifetime is way more than that. Almost 200,000 miles on my first 2007 FJR and over 100,000 on my current 2011 and never replaced any clutch component (other than fluid). Oil almost exclusively Rotella T6. I don't think the T5 has the JASO MA/MA2 rating.
 
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I am disappointed, and kind of surprised, that the shop did not do the brake fluid change. .........

Like some have said, your shop sucks. Should have replaced rotor, pads and fluid.

And some of us are surprised you're going to wait until winter to do it. Two things you don't mess with... brakes and tires. Your bike, your choice.
 
Typical FJR clutch lifetime is way more than that. Almost 200,000 miles on my first 2007 FJR and over 100,000 on my current 2011 and never replaced any clutch component (other than fluid). Oil almost exclusively Rotella T6. I don't think the T5 has the JASO MA/MA2 rating.
Same here. I have 68,000 miles on my 14ES and the clutch is as good as new. I have had two 07's in the past and never had a minute's problem with clutches. I am very easy on brakes as I down shift at all times. Having driven standard shift cars for over 40 years proper down shifting is never a problem.
 
The FJR's clutch will last indefinitely if not abused. I have a 212k FJR on its original clutch and a second with 148k on its original clutch. I had to replace a clutch at 140k once due to the abuse I gave it during a slow-speed skills class. Also had to replace another at 52k because the previous owner did not maintain the FJR well and the clutch lever was not fully returning to the full disengagement position.

Don't overthink bleeding the brakes. It's not difficult. Installing speedbleeders and especially getting the speedbleeder bag for the old fluid makes it SO much easier.
 

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