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Losing Hope


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Is it possible to get a video? Is it possible the ABS sensors got bumped around? Check all safety connections such as clutch, kickstand, etc...check your throttle/ clutch cable slack... Unplug the o2 sensor and take a quick trip around the block to see if that helps, if that helps o2 sensor is bad
 
 
As for the o2 sensor being disabled, only a few tuning products are available for the FJ-09 that disable the o2 sensor... Flashtune is not one of them AFAIK, but Flashtune now has a product you can buy to tune the closed loop area but Woolich tuning products totaly disables the o2 sensor on the FJ-09
Flashtune does have "Disable Closed Loop" which is the O2 sensor.
 
 
I had a conversation with piotrek who informed me about it...
 
The closed loop aka ecomode is pretty good itself as tuning its own range of operations and is generally left alone and left on to my knowledge... It is also my assumption if closed loop is disabled why leave the o2 sensor in and destroy it since its not being used/powered?
2012 wr250f - C-class 30+ age group
2015 fz-07- Hordpower Edition-80whp
2015 fj-09- Graves Exhaust w/Woolich tune by 2WDW @120whp
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You cannot tune the closed loop area. Hence the name 'closed'.  

https://ftecu.com/shop/yamaha-active-tune-kit/
This is not tuning closed loop. This is an auto-tune kit that uses a wide-band O2 sensor to tune fueling to your desired AFR...as long as the ECU remains in open loop.
 
Dynojet makes a kit like this also for their Power Commander. I own one.
 
If the ECU flash doesn't disable closed loop, you cannot tune that area of the fuel map.
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Flashtune does have "Disable Closed Loop" which is the O2 sensor.
...if closed loop is disabled why leave the o2 sensor in and destroy it since its not being used/powered?
 
You don't leave it in. My FZ-09 has no O2 sensor installed.
 
 
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It cant hurt to unplug the o2 sensor and see if it helps its an idea that I pulled from the FZ-07 forum where the OP posted a question with 95% similar problems...
2012 wr250f - C-class 30+ age group
2015 fz-07- Hordpower Edition-80whp
2015 fj-09- Graves Exhaust w/Woolich tune by 2WDW @120whp
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Unplug the o2 sensor and take a quick trip around the block to see if that helps, if that helps o2 sensor is bad
After I got my ECU flashed, it still wasn't as smooth as I hoped for.  I called Nels at 2WDW and he suggested that I unplug the 02 sensor, he said it wont throw a fault code and wont hurt anything.  It made quite a noticeable difference and I have ran it that way ever since. 

***2015 Candy Red FJ-09***

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...but Flashtune now has a product you can buy to tune the closed loop area...
You cannot tune the closed loop area. Hence the name 'closed'.  

 
That's not what "closed" means.
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I haven't had a chance to ride it or do anything yet, but my plan for tomorrow will be to unplug the o2 sensor and see if that yields any changes. If not, then I can start checking the cables and tps sensors and everything. But in the end, if the 02 sensor is not the problem, its something mechanical imo and will require a shop to look at it.
 
As far as the past places I've gone to, they both said the problem was somewhat fixed. They knew there was a problem before and claimed their solution had relived part of the issues...The out of house mechanic admitted he didn't have a quick diagnoses for me, and in order to get it would have to open the engine up and that takes time and money, so he said it might just be something to have to live with...not possible for me.
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Hdgunnell - I'm next to Pittsfield if you'd like to come down this way.  We could do a short loop to see what's going on.  Plus you could ride mine, which is red and therefore much faster.  Let me now if interested in next weekend for this as I am going on a trip shortly thereafter.
I'll keep that in mind, thank you. It's still a bit of a drive down their but my gf loves the Berkshires and would like to visit pittsfield sometime, so we could at least make a day of it. 
When  you say next weekend, do you mean 5/5 or 5/12?
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I haven't had a chance to ride it or do anything yet, but my plan for tomorrow will be to unplug the o2 sensor and see if that yields any changes. If not, then I can start checking the cables and tps sensors and everything. But in the end, if the 02 sensor is not the problem, its something mechanical imo and will require a shop to look at it. 
As far as the past places I've gone to, they both said the problem was somewhat fixed. They knew there was a problem before and claimed their solution had relived part of the issues...The out of house mechanic admitted he didn't have a quick diagnoses for me, and in order to get it would have to open the engine up and that takes time and money, so he said it might just be something to have to live with...not possible for me.
The only thing worse than a mechanic that doesn't  know what he's doing....  is a mechanic that doesn't know that he doesn't know what he's doing. 
BLB
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When  you say next weekend, do you mean 5/5 or 5/12?
I'm leaving on my trip the 12th.  So should now say this weekend.  As an aside, if your engine is really surging, that is not a mechanical issue.  It's controls/electronics type stuff.  Would be glad to see you on Sat, Sun or even Monday if that works for you.  Weather extended forecast isn't real encouraging though.
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I know there have been a lot of possibilities mentioned, but disconnecting the O2 sensor and adjusting the APS can be done for free, if you have the mechanical skills to take the tank off.
 
Another idea, the cam chain tensioner can go bad and cause a lot of slack in the cam chain which may cause surging, there is a Yamaha recall on that. Getting a manual tensioner is also a possible, search APE manual cam chain tensioner. But I find it hard to believe the cam chain can be that loose and still have the engine run.
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spark plugs?
...wouldn't that be funny... and possible. You'd think someone would be able to recognize that pretty easily. 
 

Gotta go back to the most simple possibility before looking into all the harder more expensive stuff IMO.
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