Intermittent Stalling, Rough Running, Hard to Start

Hello everyone,

I am a new member but have been visiting the forum since 2017. When I was trying to decide which dual sport I wanted, your comments guided me and ultimately I decided the WR was right for me. Thanks for all the insights and knowledge over the years.

My issue began last year November, when on my way to work (about 6 miles on side streets and max 45 mph zone), my bike began stalling and surging in traffic at around 25 mph. I pulled over after it completely stalled to try to determine what was happening. I couldn't find anything obvious so I started the bike and completed my commute and just managed the surging and stalling which remained intermittent for the remaining 3 miles.

After work, I rode home and the stalling/surging was no better. I took a different route where I could hit highway speeds and at 70mph, it would completely stall but then start running again. I got home, waited for the engine to cool and then pulled the spark plug. With the tuner, I figured I could have had the low speed fuel set too high and perhaps the plug was fouled. It looked okay but I replaced it anyway and reduced the fuel at both the low and mid range. This seemed to improve the condition but it did not go away completely. I noticed a clear difference in the smell of the exhaust so I figured it was running too rich and now less so. ??? This was late in the season and it was time to put it away anyway so I put it on the battery tender and left it until spring.

Fast forward to April of this year, I went to start it and nothing - original battery would no longer hold a charge - I ordered and replaced the battery in July, it cranked great but would not fire like normal. I drained the fuel and replaced with fresh. I got it running and took it for a ride but the stalling/surging was worse than before. In the last few months I did not have the time to deal with it. I am telling you this to explain why it's August and I am just getting to this. I have other bikes, my truck and my wife's car so this was not a priority.

Yesterday, (8/3/2024) I finally got the time to deal with it and decided to restore the bike to stock configuration - removed FMF, removed tuner, reversed air-box mod, etc. I figured I needed to eliminate those elements from the equation. Afterward, I started it and it ran absolutely terrible - stalling, rough through the rpm range, would not idle. Each time I started it again after stalling, it ran better until I was able to take it for a ride. I probably restarted it 5 or 6 times before it would run right. The condition was still present and completely unchanged. Note that when it was running right, it ran great but when it began stalling/surging, it was happening intermittently - it would run fine for a minute or two and then terrible. It would run badly for a few seconds and then run great again - almost like a fouled plug or faulty injector.

I brought it back to my garage and began poking around the wiring. I started it and then lightly touched the wiring harnesses and devices plugged in to the right of the battery box. I lightly touched something and the bike instantly stalled. I started it again, touched again and it instantly stalled. I was able to recreate this over and over again until I was able to say nearly definitively that there was something in that area causing this problem. After pulling everything out of this area - a few relays or sensors(?) - I unplugged/plugged a few things, wiggled the connectors on others, poked around at the wiring harnesses and could not get the bike to stall again. I took it out for a ride and it is running perfectly...

Now my question is, which one of these connectors or devices could be the cause of this?

Is it a failing relay? Is it a flaky pin on one of the connectors? Is this common and is Yamaha aware of it?

Also, is it normal for the bike to run terribly after restoring to stock config - seemed like the computer was recalibrating or something. This seemed like a normal phenomenon unrelated to the issue here and after several run/stop cycles it gradually smoothed out but of course the issue remained.

I look forward to hearing your thoughts.

Greg

Addressing some of the things you mentioned first:

gxahart52 wrote:

I got home, waited for the engine to cool and then pulled the spark plug. With the tuner, I figured I could have had the low speed fuel set too high and perhaps the plug was fouled. It looked okay but I replaced it anyway and reduced the fuel at both the low and mid range.

First of all, if you are using gasoline with Ethanol in it then plug reading is not valid.

Secondly, there are no "low" and "midrange" fuel adjustments in the EJK; the adjustments are for constant throttle (Green), acceleration (Yellow), and WOT (Red).

gxahart52 wrote:

Now my question is, which one of these connectors or devices could be the cause of this?

Too many electrical components there to be able to tell which one is responsible. If it happens again try to isolate it to a specific wire loom or component.

gxahart52 wrote:

Also, is it normal for the bike to run terribly after restoring to stock config - seemed like the computer was recalibrating or something.

Not sure what you're asking here; if your question is whether the bike surges and stalls when stock, then the answer is an obvious no. Additionally, the ECU does not have a learning function, so it will never calibrate or re-calibrate; it simply responds to the inputs it receives from the various sensors and the maps it has in its memory.

For the actual troubleshooting:

Did the bike throw a Fault Code? Since it has been a long time since the original failure occurred, go to Diagnostic Monitoring Code 61, look at all the accumulated FCs, and determine whether these could explain what you experienced (or post them here).

Thanks Johnkol.

I appreciate the clarifications on the tuner - that makes sense given the limited inputs and I think throttle position is one of them. Of course, removing it and finding the problem persisted without it removes it completely from the equation.

I know I provided a lot of context and probably too much information in my initial post. I am so certain that there was something flaky going on to the right of the battery box that I thought I should post a pic of exactly what I touched to make it stall over and over again. Perhaps this will narrow down what that "device" is or what part of the harness might have been involved.

I hope I did this right.

The blue arrow is pointing at a little black box on a harness. This is what I touched multiple times and at each touch, the bike stalled. I couldn't figure out how to unplug it. It was one of the things I just gently pulled on and pushed on to ensure it was seated. Others I unplugged completely and pugged back in.

The problem is, after doing all this, I could not recreate the stalling issue and the bike is now running perfectly. Basically, I don't think I can trust the bike until I have a better handle on what the issue was in the first place.

I will check for fault codes. I never saw a check engine light or any other sign other than the poor running.

Thanks again for the feedback.

gxahart52 wrote:

The blue arrow is pointing at a little black box on a harness. This is what I touched multiple times and at each touch, the bike stalled.

The component where the thick black and red cables go is the starter relay (and main fuse), but I'm not sure if your blue arrow is pointing to that or to  something else behind the starter relay. Given that the issue is intermittent, I would suspect a ground wire not making good contact, or a frayed wire in that loom.

The only thing I can suggest is to take all these components out of there, unplug as many as you can, and take a very close look at every electrical connection.

BTW, did you install those white zip ties (top of the picture) that cinch the wire loom to the frame? These are not OEM, which means that either you or the previous owner had to take this wire loom apart, pointing to this problem having been there for some time.

johnkol wrote:

The component where the thick black and red cables go is the starter relay (and main fuse), but I'm not sure if your blue arrow is pointing to that or to  something else behind the starter relay. Given that the issue is intermittent, I would suspect a ground wire not making good contact, or a frayed wire in that loom.

The tip of the blue arrow is on top of the component. It's about the size of a sugar cube. I will get a better pic with it pulled out soon.

johnkol wrote:

The only thing I can suggest is to take all these components out of there, unplug as many as you can, and take a very close look at every electrical connection.

I did this already but I think I can do better. I already inspected all the wiring in the suspect area and it all looks perfect. I was unable to pull the suspect component off the harness - I couldn't figure out how - it does not have the normal latch found on all the others and almost looks like a cap on an unused connector.

johnkol wrote:

BTW, did you install those white zip ties (top of the picture) that cinch the wire loom to the frame? These are not OEM, which means that either you or the previous owner had to take this wire loom apart, pointing to this problem having been there for some time.

I'm the original owner. I probably snipped the original ones when I put on the rear taillight/signal assembly and the front hand guard signal lights. I think I removed them to open the path to feed the wires through and replaced them with what I had. I did every mod myself and I am super anal. I'm pretty sure this is component related but I will follow your advice and look more carefully at the entire loom where possible.

I will dig into this a bit more and provide better pics probably tomorrow.

Thanks!

Since you're the original owner disregard my comment about possible prior damage to the wire loom.

gxahart52 wrote:

The tip of the blue arrow is on top of the component. It's about the size of a sugar cube.

There is no such sugar-cube-sized component in that area; there is the starter relay where the thick black and red cables go, and to the left of it is a relay unit for multiple components. Behind that relay, on the airbox wall, is the air temperature sensor connector, with the sensor itself inside the airbox.

Maybe while you were re-arranging the wire loom another component ended up there?

https://servimg.com/view/20575834/2

This is it.

gxahart52 wrote:

https://servimg.com/view/20575834/2

This is it.

This is just a wire connector, part of the larger wire loom. Open it up and examine the wires, there is probably either corrosion or some wire(s) may have frayed.

Thanks again Johnkol for your time reading/responding.

I finally had the time to get the DTC's and there is one. In the DIAG DT61 is "15" (Throttle Position short?) and DT62 shows "1". Not sure if the 1 means it repeated only once - the condition happened at least 20 times or more. It could also have been thrown when I was running the bike and disconnecting things to try to recreate the condition. While riding it and experiencing the stalling, I never saw the check engine light but it is also possible it had cleared by the time I looked. This is still a mystery until I find something definitive. We could be on to something with this throttle position sensor fault and it would be great to hear your thoughts.

I took it out yesterday for a 40+ mile ride at various speeds and it was perfect. I guess every time it gets me home without an issue adds to my comfort that it is fine now and was only a flaky connection.

I will keep looking for the smoking gun... and if I find it, I will let you know. I will probably focus on the throttle position sensor wires and chase them back to the ECU.

gxahart52 wrote:

I finally had the time to get the DTC's and there is one. In the DIAG DT61 is "15" (Throttle Position short?) and DT62 shows "1". Not sure if the 1 means it repeated only once - the condition happened at least 20 times or more.

The "1" in DMC 62 is just a memory location, does not indicate how many times the Fault Code has been thrown.

Given that we don't know when this Fault Code was thrown, go ahead and erase it by going to DMC 62 and turning the engine stop switch to On. If there is a problem with the TPS, the ECU will throw FC 15 again and you can capture it.

Did you take the wire connector apart to see if there is corrosion or a frayed wire?

I did not strip back any casing but I gently pulled it back where I could. My eyesight is not great anymore but I am pretty confident there are no bare or otherwise damaged wires where I was able to see them in the loom.

I also pulled apart the connectors again to the right of the battery box to look for corrosion and pins that were not fully engaged in the harness connector but they all looked perfect. I pulled the fuel tank and checked the TPS connector as well - looks perfect.

I cleared the codes and have been riding it every day since this past Saturday and so far the condition has not resurfaced - it is running perfectly.

If it resurfaces, I will check the DTCs right away. If I cannot find the smoking gun quickly, I'm done. I will take it in.

Hello everyone,

I finally have an update:

I added about 150 miles since my last post riding around the neighborhood and back and forth to work. It had been perfect until today. The problem resurfaced about a mile from work and then stalled several times while navigating to my parking spot.

When I left work, it started and was perfect all the way home (about 6 miles).

I went back to the "sugar-cube" and poked at it like before. I was able to recreate the condition described earlier in this thread where I could touch it and make it stall, over and over again. I popped off the cap and discovered there is a 6-pin shorting block basically acting like a wire-nut on 6 wires entering the connector. It appears that one of the wires is not terminated well and is making intermittent contact.

I'm not sure how I'm going to fix it yet but the good news is - this is the smoking gun and the mystery is solved.

gxahart52 wrote:

I went back to the "sugar-cube" and poked at it like before. I was able to recreate the condition described earlier in this thread where I could touch it and make it stall, over and over again. I popped off the cap and discovered there is a 6-pin shorting block basically acting like a wire-nut on 6 wires entering the connector. It appears that one of the wires is not terminated well and is making intermittent contact.

Right, and we said previously that this "sugar cube" is a wire connector and you would need to take it apart to ascertain which of the wires is not making good contact.

You now seem to have disassembled the wire connector, so you should be able to pull the wires and see which one is damaged, and what the specific damage is.

Hello everyone,

I pulled apart the harness and freed the connector giving me some slack to work on it.

There are 6 wires terminated in the connector and one of them when lightly touched, would stall the engine. I released the terminal (female pin) from the connector and pulled it out to inspect it. It looked fine, the copper was clean and well crimped. When I slid the male pin into it however, it was very loose - slid in easily and I felt no friction when pushing it in and out.

I found the spring that provides the friction on the male pin was cracked at the end and was no longer providing the pressure required to keep a tight connection.

I don't have a replacement pin so for now I just lightly crushed the terminal end so it would connect tightly and I put it back together. Fixed, but not perfect. I could get a new pin and fix this right or I could replace this connector with a heat-shrink wire terminal like this one.

https://www.jttproducts.com/store/p/4640-Heat-Shrink-Crimp-Seal-Closed-End-Connectors.aspx

Does anyone here have an opinion on why Yamaha uses these connectors where a high quality waterproof splice would have sufficed? I found two more of them wrapped with tape and it seems a potentially troublesome, built-in fail-point with no obvious reason for it.

gxahart52 wrote:

Does anyone here have an opinion on why Yamaha uses these connectors where a high quality waterproof splice would have sufficed?

It's not just Yamaha, you cannot use soldering or heat shrinking on any production floor due to worker safety and manufacturing repeatability.

Thanks again Johnkol for your guidance. I think I will replace the pin. Its an opportunity to buy another tool!

My comment was not intended to dissuade you from soldering wires, it was merely an explanation of why soldering or heat shrinking can never be part of a manufacturing process. You are not manufacturing, so you have the option to use heat shrink soldering rather than crimping.

Right. I didn't take it that way either. I am just not a fan of cutting and modifying the factory harness regardless of if I think it improves it in some way. I considered it and figured it is a very easy repair either way.

Despite the bad luck I experienced, the WR otherwise has an incredible track record of reliability. Unless a lot of other owners were experiencing problems with these connectors and broken pin springs, I would just as soon repair it exactly as it came from the factory. Wiring mods tends to scare people at resale. (Not that I have any intentions of selling this bike).

I was able to find the entire connector with pins for $2 + $15 shipping. I found that I had the tool already. I figure 30 minutes and this will be in the past like it never happened. haha..