Surging, Sputtering at 4,000-5,000 RPM

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JerrySuhrstedt

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I have a 2006 AE with only 6,000 miles on it.  My buddy I bought it from let it sit for too long.  When I shift in to 2nd gear and hold the throttle at around 4000 RPM, the engine power is intermittent and sort of surges.

Where should I start looking?  New plugs?  Fuel Injection?  I've already ran 2 cans of Seafoam through it over the course of 4 tanks of gas.

 
When you change up into 2nd, are you dipping the throttle to allow the engine revs to match the road speed? If not, the MCU will slip the clutch and attempt to reduce engine power by retarding the ignition.

It will do this until the speeds match, either by you reducing the throttle or the bike accelerating to a matching speed in the new gear (meanwhile hammering the clutch). 

 
When you change up into 2nd, are you dipping the throttle to allow the engine revs to match the road speed? If not, the MCU will slip the clutch and attempt to reduce engine power by retarding the ignition.

It will do this until the speeds match, either by you reducing the throttle or the bike accelerating to a matching speed in the new gear (meanwhile hammering the clutch). 
Hmmm... guess I don't understand that.  My bike has the YSS automatic clutch... does that make a difference?  I'm just saying that if I continue holding my throttle in 2nd or 3rd gear at around 4000-5000 RPM and then continue to hold it there... the engine is not constant.  It's like something is plugged and allowing intermittent fuel to get through.  So it gives me intermittent power and the bike feels like it's jerking and not smooth.

With all that being said, your theory may be what I'm experiencing... I don't know.

 
As you haven't said "No, it's not that", I will expand a bit.

Remember that the clutch and gearbox are the same as on the manually controlled bikes. The clutch is operated by a motor that disengages it when you change gear, then re-engages it in the new gear. But it doesn't just drop in the clutch any more than would a rider while holding the throttle at high engine revs (unless he wanted to attempt a wheelie or make the rear tyre skip!).

On a bike with conventional controls, when you change up you would momentarily dip the throttle as you pull the clutch, change gear, then open the throttle as you re-engage the clutch, this allows the engine revs to match the new gear road speed. With your Gen 2 YCC-S, the bike has no direct control on the throttle, so if you don't allow the engine to match the new gear road speed, the MCU will hold the clutch slipping. This allows some torque through the clutch, meanwhile doing its best to reduce engine power by retarding the ignition. Crude, but it's all the control over the engine power it has. Makes for a very tardy gear-change (and not very kind to the clutch plates), but it does protect the rider from the rear tyre losing grip if he changes gear without proper throttle control in a slippery corner.

When you change up, learn to momentarily dip the throttle as you flip the switch (I never use the foot change, just my fore-finger to change up or down), or blip the throttle open a bit as you change down, just as you would for a smooth change on a conventional bike. Remember, you are always trying to reduce the torque in the gearbox whilst changing gear.

The throttle dip or blip is only for a fraction of a second. It takes a little practice to get the timing right, but it will become second nature. You will be rewarded by pretty much the smoothest, quickest gear-change you've ever come across on a bike.

As an aside, I mentioned that I only use my forefinger to change gear. To expand a bit on that, different riders have different preferences. A fairly common one is to use the finger to change up and the foot lever to change down. On my first YCC-S bike, I chose to deliberately not use the foot lever so that I had a reminder that, if I rode a conventional bike where I had to use the foot lever, I needed to use the clutch! I first started using forefinger to change up and thumb to change down. But I found this clumsy, and frequently sounded the horn instead of changing down. Finally I ended up using my forefinger either pulling or pushing the finger part of the switch, makes for very rapid up and down changes. I've always preferred to stick with the finger, leaving the foot completely free for putting down when coming to rest. The finger is also better at timing than the foot.

Not directly relevant, but just to add that having had two Gen 2 YCC-S bikes, I am now fortunate enough to have a Gen 3, unavailable as a YCC-S in America. It takes advantage of its throttle-by-wire and you don't need to adjust the throttle manually, it does this for you, optimising throttle and clutch during any normal change. 

 
Sounds like it could be more related to fuel delivery or ignition than the YCCS since it isn't a momentary behavior just after shifting.   A few possibilities that I can think of...

Fuel injectors - you might want to pull them and take them to a shop that cleans and tests them.

Fuel pressure - not likely but you could check.

Plugs - change them.

Wires - first make sure that they are pushed down all the way on the plugs.  Sometimes an issue where the cap and wire are not making good contact.  The cap has sort of a sharp spike that screws into the wire core.  You can unscrew the cap, trim off 1/4" of wire and screw caps back on.  Wire end sometimes gets corroded or contact diminished from careless pulling wires off the plugs.  Don't trim much wire - Yamaha doesn't have much to spare.  A little smear of silicone grease where the cap meets the engine makes future removal easier.

Coils - a possibility but not common.

Lean Yamaha fuelling.  This is not an adjustment you can make directly. You can consider a Power Commander to richen up the mixture to smooth things out or do Ivan's ECU flash.  Note: I had a PC III on my '07 and it was smoother at 4000 rpm after I removed it although it improved low rpm throttle response at the expense of poorer fuel economy. It came with the bike and I didn't play much with settings...

Good luck.

 
 I'm just saying that if I continue holding my throttle in 2nd or 3rd gear at around 4000-5000 RPM and then continue to hold it there... the engine is not constant.  It's like something is plugged and allowing intermittent fuel to get through.  So it gives me intermittent power and the bike feels like it's jerking and not smooth.
I've never owned an AE but assuming here they use a TPS like all the others?  If so give that a look-see.  With only 6000 miles it shouldn't be too worn but the symptoms you describe match the issue.  As a check you should be able to replicate the jerking and stumble whenever you hit the same RPM range in any gear at any speed with it becoming more pronounced as the bike gets hotter.  But again, no idea how the AE component affects all this.

Check this link for further info.  Search out many other threads here on this also.

 
start with the EZ stuff I would guess. Check all hoses under tank, plug wires, critters in air filter (fun, getting that one out on an AE), battery voltage running. Doubt plugs bad or sync out with such low mileage.

 
By all means, check the TPS range as per the service manual.  Easy to check and adjust.  If there is a real dead spot, it will show up as you rotate the throttle but it usually isn't that obvious.  A bad Throttle Position Sensor is possible but was more of an issue with Gen I and Gen III.

Did you check for stored ECU codes?

 
TPS can be cleaned with contact cleaner it take about 20 once you know what to do.
If it is simply dirty, I fully agree.  Ionbeam did some TPS autopsies on failed Gen I and Gen III TPS units.  The mode of failure was worn resistive material that the "wiper" traversed.  This was the result of the Gen III one.

https://www.fjrforum.com/topic/169700-anatomy-of-gen-iii-fly-by-wire-tps/?tab=comments#comment-1335495

This is the Gen I dissection.

https://www.fjrforum.com/topic/12074-anatomy-of-a-tps/?tab=comments#comment-148013

In both instances, it was physical failure rather than "dirt".  Some of the 2005 model year were recalled because of defective TPS.  Few issues with Gen II.

Thread on TPS recall for later Gen I...

https://www.fjrforum.com/topic/122278-fjrf0061-throttle-position-sensor-tps/

 
How bad is it? It may be normal lean fuel mapping. 
That was included in my initial response.  I would want to rule out everything else first in case there is a real fixable mechanical issue.  A Power Commander or an "Ivan's ECU flash" would be the ticket if it is a normal lean stumble.  https://www.fjrforum.com/topic/177589-gen-ii-ecu-reflash-by-ivan/

I would suggest that it would be a good idea to get the opinion of someone who has some experience with early Gen II FJRs.  Even if it is "normal", it might be improved with the fueling changes.  Yamaha fuel mapping improved after 2007; my 2011 is way better than my 2007 was although the greatest issues were at low throttle openings, not at 4000-5000 rpm.

 
If it is simply dirty, I fully agree.  Ionbeam did some TPS autopsies on failed Gen I and Gen III TPS units.  The mode of failure was worn resistive material that the "wiper" traversed.  This was the result of the Gen III one.

https://www.fjrforum.com/topic/169700-anatomy-of-gen-iii-fly-by-wire-tps/?tab=comments#comment-1335495

This is the Gen I dissection.

https://www.fjrforum.com/topic/12074-anatomy-of-a-tps/?tab=comments#comment-148013

In both instances, it was physical failure rather than "dirt".  Some of the 2005 model year were recalled because of defective TPS.  Few issues with Gen II.

Thread on TPS recall for later Gen I...

https://www.fjrforum.com/topic/122278-fjrf0061-throttle-position-sensor-tps/
I can only give my own experience I have cleaned the TPS three times, it seems to need cleaning after 18,000 - 22,000 miles and after cleaning it's a s smooth as a babies bum.

 
That was included in my initial response.  I would want to rule out everything else first in case there is a real fixable mechanical issue.  A Power Commander or an "Ivan's ECU flash" would be the ticket if it is a normal lean stumble.  https://www.fjrforum.com/topic/177589-gen-ii-ecu-reflash-by-ivan/

I would suggest that it would be a good idea to get the opinion of someone who has some experience with early Gen II FJRs.  Even if it is "normal", it might be improved with the fueling changes.  Yamaha fuel mapping improved after 2007; my 2011 is way better than my 2007 was although the greatest issues were at low throttle openings, not at 4000-5000 rpm.
I get it and all your  info is good and accurate.  I'm just giving my opinion. My 07 was like that and I had to ride around  it. In light load situations in 2nd or 3rd gear, shift into 4th and put a load on it. It may help with the lean surge. Just an idea if it turns out all else is ok.

 
I'm no expert but I've had my Feej for 16 years and what I've discovered is that they hate old fuel. Your symptoms pretty much describe what I discovered early on. My bike bucked, surged, sputtered, check engine lights,..the whole magilla. That was when I'd take it out in the spring after sitting mostly through the winter in the garage with October gasoline in the tank. 

I put some fresh gas in it along with a can of Sea Foam and  the bike evens out like nothing ever happened.  YMMV...🙂

 
That was included in my initial response.  I would want to rule out everything else first in case there is a real fixable mechanical issue.  A Power Commander or an "Ivan's ECU flash" would be the ticket if it is a normal lean stumble.  https://www.fjrforum.com/topic/177589-gen-ii-ecu-reflash-by-ivan/

I would suggest that it would be a good idea to get the opinion of someone who has some experience with early Gen II FJRs.  Even if it is "normal", it might be improved with the fueling changes.  Yamaha fuel mapping improved after 2007; my 2011 is way better than my 2007 was although the greatest issues were at low throttle openings, not at 4000-5000 rpm.
Yes I just got my ECU back from Ivan... had it flashed.  Just going by how my bike feels... kind of feels like the ethanol in gasoline has plugged things up.  I think I'm going to start with new spark plugs, then move from there.

 
I'm no expert but I've had my Feej for 16 years and what I've discovered is that they hate old fuel. Your symptoms pretty much describe what I discovered early on. My bike bucked, surged, sputtered, check engine lights,..the whole magilla. That was when I'd take it out in the spring after sitting mostly through the winter in the garage with October gasoline in the tank. 

I put some fresh gas in it along with a can of Sea Foam and  the bike evens out like nothing ever happened.  YMMV...🙂
Yes so far over the past couple of weeks I have ran 2 cans of Seafoam thru my gas tank... probably 4 tanks of gas.  Didn't fix it.  But yeah, I was thinking the same thing.

 

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