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Update on the other one..... replaced TPS, still same problem. APS replace is likely next, so we'll see if that does it. Again, his is different, he's getting a jump in rpm, not surge, although I'm thinking the APS can cause either. Unfortunately tossing $$ at it and hoping......
The APS is on the underside of Gen3-up throttle bodies, necessary for throttle by wire as an ECU input. Very similar to a TPS but different.

I thought the TPS on that year had throttle position and the 2nd circuit was fly by wire. Why does the ECU need another input hooked to throttle for acceleration?

Gen III -- The Throttle Position Sensor is mechanically locked to the throttle plate rod and reads the true position of the throttle plates. When the rider twists the handlebar throttle the throttle cable moves a spring tensioned pivot which is attached to the Accelerator Position Sensor (APS). The spring tensioned pivot is what gives the throttle its feel and spring return. The voltage from the APS is fed to the ECU which uses all the sensors to determine what is to happen every 1/1000 second. The ECU then actuates the Throttle Servo Motor to move the throttle plates the required amount at the required speed. This is the YCC-T (Yamaha Chip Controlled Throttle) loop.

All earlier GENs, the handlebar throttle directly actuated the throttle plates, in the YCC-T bikes the handlebar throttle only actuates the APS. The Throttle Servo Motor is what actually operates the throttle plates.

This thread has more than one kind of surging going on. It occurs to me that the APS can be verified on the bike if the surging is happening at a particular rpm range. Set the cruise control below the rpm range where the surging is happening, then use the Resume to bump the speed up through the surging range. When the cruise is set the APS is not in play. If the surge is gone with the cruise on, it's the APS. If the surge is still there you now know it's not the APS. Search on.

ionbeam wrote: ↑Fri Apr 30, 2021 2:10 pm This thread has more than one kind of surging going on. It occurs to me that the APS can be verified on the bike if the surging is happening at a particular rpm range. Set the cruise control below the rpm range where the surging is happening, then use the Resume to bump the speed up through the surging range. When the cruise is set the APS is not in play. If the surge is gone with the cruise on, it's the APS. If the surge is still there you now know it's not the APS. Search on.

You must do this for a living...

I guess I understand, but it seems like a whole lot of extra crap. You need a throttle cable to make the rider have something he's used to twisting? A throttle tube grip sensor and a TPS to the ECU, and a servo is enough. You really need microsecond servo movement of the throttle? Can a mortal feel the difference in response between Gen I,II and Fly by wire?

If I didn't hate jets (and float bowls) and love laptop tuning FI, I'd still be ok with carbs.
(Maybe not)

Powerman wrote: ↑Fri Apr 30, 2021 6:16 pm I guess I understand, but it seems like a whole lot of extra crap. You need a throttle cable to make the rider have something he's used to twisting? A throttle tube grip sensor and a TPS to the ECU, and a servo is enough. You really need microsecond servo movement of the throttle? Can a mortal feel the difference in response between Gen I,II and Fly by wire?

If I didn't hate jets (and float bowls) and love laptop tuning FI, I'd still be ok with carbs.
(Maybe not)

Probably easier and cheaper to have the return spring and TPS not mounted on throttle tube.

Difference between Gen 2 and Gen 3 throttle response? Yes. A "Touring" mode would be more difficult to implement, and some riders like this mode (personally I use it extremely rarely). "Sport" mode is very similar to Gen 2, but I suspect it does boost the response a bit if you open the throttle very rapidly - just a suspicion on my part after it lifted the front wheel, I've never done that on my Gen 2s.

Of course, cruise control and traction control are very easy to implement once you have throttle by wire.

One more advantage of throttle by wire, it is significantly lighter to operate, it's only working against a (lighter) return spring.

Powerman wrote: ↑Fri Apr 30, 2021 6:16 pm I guess I understand, but it seems like a whole lot of extra crap. You need a throttle cable to make the rider have something he's used to twisting? A throttle tube grip sensor and a TPS to the ECU, and a servo is enough. You really need microsecond servo movement of the throttle? Can a mortal feel the difference in response between Gen I,II and Fly by wire?

If I didn't hate jets (and float bowls) and love laptop tuning FI, I'd still be ok with carbs.
(Maybe not)

+1 to mcatrophy The throttle difference between my Gen I and my Gen III is significantly better.

The fastest conscious human reactions are around 0.15 s, but most are around 0.2 s. Unconscious, or reflex, actions are much faster, around 0.08 s because the signal doesn't have to go via the brain. By making the YCC-T reactions 1µs it keeps the operation feeling smooth, without any notchiness. These days, 1µs is, yawn, slow.

Yamaha brags:

The ECU contains two CPUs with a capacity about five times that of conventional units, making it possible for the system to respond extremely quickly to the slightest adjustments made by the rider. In particular, optimized control of the throttle valve opening provides the optimum volume of intake air for easy-to-use torque, even in a high-revving engine.

Yamaha goes on to brag:

Update on the other surger.....

" was able to get out and pay closer attention to the issue. In 1st and 2nd, i stop twisting the grip at above 3000 rpm and the bike will accelerate on its own up to about 4500 rpm. Below 3000 and about 4500, i still have good throttle reponse.
In 3rd gear i put CC on and was able to increase mph steadily in 1 mph increments from 30 mph on up. But i was also able to do this manually with the grip. The surging doesn't seem to be an issue in 3rd 4th or 5th gear."

Bike surges with or without cruise control on.

That mean anything to anyone?

Not particularly.... except the APS is maybe still in play, cruise or not. Is it more noticeable in any particular gear, or in other words, does it not surge in certain gears? Never mind, I re-read post 1 again..... I'm voting an APS change or Cylinder Identification Sensor change.

Potentially related, a Gen1 owner had a surging idle issue, with or without Cylinder Identification Sensor plugged in.... now that is unique to Gen1 that you can have it unplugged and the bike even start, not so on Gen2/3. Anyway, AFAIK it tested OK, but he replaced the CIS and all was cured for his idle surge.

My ‘13 Jolene surges from 3,000 to 4,000 RPM in any gear. It’s especially noticeable when I gently let off the throttle, like when entering a turn. Then I can feel her rocking back and forth beneath me. Incredibly unnerving on those long, sweeping 3rd gear curves. Even worse in 2nd gear where the Gen III throttle is so responsive in Sport Mode. I thought I had thrown every part at it except the APS, that’s next. But now I hear of a CIS? Sheesh this is getting old.

Unfortunately, at this point, there is not much to do but throw new parts at it. CIS is an easy replace. APS a PITA. It's a bummer the TPS didn't fix it, that seemed more like the obvious solution.
(no update from the other guy.......).
Meanwhile, Touring mode might tame down the throttle response...... have you adjusted the throttle freeplay to near zero by chance?

My gut is telling me vacuum or injector. Any thoughts on that?

I'd hate for it to be an injector, that means Bust would have been right from the beginning. If that's the case, look for a bad things to happen in the universe.

It's only money...... you could send the injectors out to be cleaned and flow test report... $100-ish. Or if you wanna take a wild guess, pull the injectors and activate them via the diagnostic menu. You can watch them spray. But, won't tell you much, need the flow test.

Vacuum off the table in your opinion?

Festus wrote: ↑Tue May 18, 2021 9:26 am My gut is telling me vacuum or injector. Any thoughts on that?

I'd hate for it to be an injector, that means Bust would have been right from the beginning. If that's the case, look for a bad things to happen in the universe.

Viper_Dad wrote: ↑Mon May 17, 2021 10:58 pm My ‘13 Jolene surges from 3,000 to 4,000 RPM in any gear. It’s especially noticeable when I gently let off the throttle...I thought I had thrown every part at it except the APS, that’s next. But now I hear of a CIS? Sheesh this is getting old.

Festus wrote: ↑Tue May 18, 2021 9:26 am My gut is telling me vacuum or injector. Any thoughts on that?

With the surging happening in a narrow RPM range, IMO, vacuum is off the table. In a car with an EGR, vacuum could be suspect but not the FJR.

Injector issues can't be ruled out, but again, in a narrow RPM range the injectors are highly unlikely.

So, here are the major players in the engine management, based on symptoms we can rule out a lot of things:

High voltage ignition
coils

Fuel System
fuel pump
fuel filter
injectors

Air System
Air filter

Control System (ECU and sensors)
Coolant temp sensor
Cylinder identification sensor
ECU
Throttle position sensor
Accelerator position sensor
Rear wheel sensor
Lean angle sensor
Air temperature sensor
O2 sensor
Catalytic converter
Crankshaft position sensor
Throttle Body servo
Intake air pressure sensor

I've highlighted the sensors that are most likely to cause narrow band surging. In a nod to Ray I kind of highlighted the Cylinder Identification Sensor. The CIS is a simple digital ON/OFF item, if the ECU senses anything wrong with the CIS it will flash the Engine Warning light at the time of the failure. The CIS is a 'Fail Safe' item, if it fails while riding you will get a warning light but the bike is ABLE to drive. If the CIS is bad the bike is UNABLE to start.

The surging isn't really a fuel injector related failure. Usually a FI issue would come with other operational issues.

The TPS should be a known good item. It would be interesting to monitor the new TPS while riding. (Can you replicate the surging on the center stand, in neutral?) If the TPS shows NO surging movement of the throttle plates during surging it's not the TPS or APS. If the TPS shows fluttering throttle plates it almost has to be the APS or servo motor. The simple place to start would be the APS.

I haven't looked 'under the hood' to see how easy/hard it would be to back-probe the APS to check for operation. Like the TPS, if it's bad it will be obvious on a meter during the time of surging.

My 06 is surging between 2-3K when lightly loaded. Crank on it and it goes through that spot smoothly.

'06-'07 had that as a feature.......