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New "Hiccup" on a 2015 FJ-09


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Good idea FJR.
A safer way would be to come to stop in gear with the clutch pulled in, and put the side stand out with left foot. (Driveway, parking lot, garage, etc)
 
Bike should die immediately.
This DTC seems to set at unexpected times, however. In fact, Yamaha has published something about that here in the US.
 
-S
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Update:
 
I have done the tb sync and thought that the problem may be corrected, but I was wrong. I have ridden the bike numerous times since the sync, varying weather and this morning the temps were much cooler and the bike started having issues again. I watched and any time that it "hiccuped" I was between 4700 - 5000 rpm. It didn't matter if I was maintenance throttle or accelerating. I tried it in Std mode and A mode and still the same results. I checked for codes and there are none. I will be adjusting the TPS(APS) this weekend to see if that helps.
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Update: 
I have done the tb sync and thought that the problem may be corrected, but I was wrong. I have ridden the bike numerous times since the sync, varying weather and this morning the temps were much cooler and the bike started having issues again. I watched and any time that it "hiccuped" I was between 4700 - 5000 rpm. It didn't matter if I was maintenance throttle or accelerating. I tried it in Std mode and A mode and still the same results. I checked for codes and there are none. I will be adjusting the TPS(APS) this weekend to see if that helps.
 
Rather than looking at the rev range try looking at the throttle position. And when you are adjusting the APS look very carefully at this range in the meter. Hopefully you will see a dead spot and that is your issue. It is possible the wiper in the TPS or APS is slightly dirty or damaged. Also water in the fuel is another common cause of that. (But not rpm dependent)
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Update: 
I have done the tb sync and thought that the problem may be corrected, but I was wrong. I have ridden the bike numerous times since the sync, varying weather and this morning the temps were much cooler and the bike started having issues again. I watched and any time that it "hiccuped" I was between 4700 - 5000 rpm. It didn't matter if I was maintenance throttle or accelerating. I tried it in Std mode and A mode and still the same results. I checked for codes and there are none. I will be adjusting the TPS(APS) this weekend to see if that helps.
Rather than looking at the rev range try looking at the throttle position. And when you are adjusting the APS look very carefully at this range in the meter. Hopefully you will see a dead spot and that is your issue. It is possible the wiper in the TPS or APS is slightly dirty or damaged. Also water in the fuel is another common cause of that. (But not rpm dependent)
When you say look at the throttle position, is this something I can do while riding?  I don't think it's water in the fuel as it has happened through several tanks of gas, from different stations.  
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I had a sudden and very brief surge then flame out while doing close-quarters battle during rush-hour at 70mph. Nothing seemingly wrong after the fact. But it might have been due to a loose ground wire. Revisit the major junctions and remove and inspect the battery connections and as a test, disconnect and manually short the side-stand switch and ride the bike that way for several days/weeks.
 
It appears that with recent bikes, if the bike is in gear and you put the side stand down the ECU has been programmed to kill the engine. My older bikes did no such thing. It might be a Euro regulation that mandates this.
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Bear in mind that the meter reading may not be sensitive enough to turn up a bad TPS/APS because the ECM has to process the signal it receives back from the sensor and then input a value on the IC.
 
More accurate to either monitor the voltage signal after it is changed by the sensor (backprobe with VOM) or ohm it out while slowly rotating the sensor through its travel especially at the area in question. You’ll be able to detect a possible “break” in the signal that way.
 
Batgirl - have you rechecked for codes?
 
-Skip
 
 
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