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I have not read any reports of dealers fixing the surging problem under warranty, you probably have to go with after market electronic add-ons like Kev's controller or ECU reflash, and APS adjustment. All the info you need is on this forum, just search for it. 
https://fj-09.org/thread/5045/accelerator-position-sensor-aps-adjustment
This is APS adjustment thread.
 
Two more ideas, throttle body synch may help, but some guys can go 8,000 miles before it needs to be done, some guys need it at 600 miles.
 
One of the big improvements is a reflash to  turn off the air injection system. IF  I remember correctly the air injection system can also cause surging as the ECU changes back and forth from open to closed mode.  I cannot remember the details, but that will send you looking in the right direction.  Hopefully, someone with better memory and saved links will post up better info for you.

Thanks, and yes I searched some of the info.  I was just wondering if they would fix it under warranty.  I am irritated as when I bought my bike, I talked to the service dept and they told me they checked the throttle body synch at the 600 mile service.  When I took it in, there were different folks and they said oh no.  That's not til the 4000 mile service.  So I paid $190 for an oil change and chain adjustment.  Oh well, at least I have a piece of paper that says they did the 600 mile service...... I have a Morgan Carb tune, I'll check the throttle body synch myself.  If that doesn't fix it, i'll go the other routes.  
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I've not had my FJ for very long, just had the 600 mile service done.  I've noticed the surging more and more in the last week.  The dealer said I can leave it with them and they will contact Yamaha.  I didn't, told them I would wait a week or 2.  Has anyone had this taken care of under the warranty? 

Check chain slack...should be about 1-1.5inches...  
Also be aware it's a ride by wire system, super quick electronic qizmos compared to the reg ole cable systems , at low rpms let's say cruising in 5th gear at 35mph yea I notice a little tiny surge...but 75% of the time I cruise in 3nd gear at 35mph and it's steady, smooth engine ...this is even with a tuned ECU by 2WDW using Woolich Racing software, blocked off AIS, Graves Exhaust... 
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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My FJ has a little surge at low speeds. It seems to be getting smoother the more miles I put on it. I did a throttle sync at 600 miles and checked it again at 3200 and it was well within spec. It doesn't bother me and I have had other EFI bikes that did the same thing.
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Kev's O2 mod worked wonders for me. So much so that although I would like to get an ECU flash I am having a hard time justifying the $$$
2015 Red FJ 09
2013 WR250R - little boy blue - sold
2012 DL650 V Strom - sold
2007 FZ6 - sold
1986 FJ600 - sold
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