Poor running FJR1300AE

HI Guys, I want to put a question out here to see if someone else may have experienced the same issue I am having with my FJR.

2007 FJR1300AE

The bike has 29,000 miles and has always run flawlessly. Recently, I stopped to get fuel, at the same place I always get fuel, and within a few miles the bike started to sputter. Had sort of a mis to it. It didn't want to idle and at steady throttle, you could feel a hiccup where it used to be smooth.

It was due for service, so I took it to the shop for valve service and all the major work along with the diagnosis of my problem.

At first it semed to be just possibly some bad fuel. Drained the fuel and put in fresh from another source and the problem was still there.

Compression is good- same on all 4

Valves all within factory spec

New spark plugs

New air filter

Throttlebodies synced

And the problem still exists. there are no error codes thrown to the dash.

TPS is working according to the manual

The shop removed the fuel screws on each throttle body, found some gummy residue, cleaned each one and same problem.

Removed each injector- cleaned and blew through while open- same problem.

The bike starts fine ad idles, until it warms to the 2-3 bar on the temp guage, then it will start to mis.

The exhaust pipes are all a consistent temp to each other so it is hard to isolate if it is one particular cyl.

It will idle, but has a very prominent mis while idling, and if you rev, you can hear it missing as well.

Checked all the connections on the coils, they are tight, and all the spark plugs seem to be burning exactly the same.

I checked with Yamaha for any recalls and all have been performed on this bike.

We are leaning toward a sensor of some sort giving a bad signal, but shouldn't a bad sensor throw an error code?

How about a bad ECU? Has anyone ever experienced a bad ECU?

Thanks in advance guys, I am afraid the next step is to start changing parts out 1 at a time.

Have you confirmed the battery terminals and fuses are clean, tight etc?

Check the condition of the air filter assembly. There's a small wire for the air temp sensor that can get pinched/damaged, although that should show an error code.

Check the little rubber things on the air bypass nipples used when doing TBS.

Check for air leaks using some starter fluid spray around the intake area whilst engine is running

Check the cold start circuit is operating as it should

I just had the same thing happen to me. Idled like crap, accelerated fine, had a miss at constant throttle. Check the battery connections. I thought for sure it couldn't be that because I never lost the clock or anything like that. Opened things up and sure enough the negative cable was just lying on the terminal with the screw completely loose. It's an easy check that only takes 5 minutes. Best of luck and I hope yours is as easy a fix as mine was.

Burns1

Bad battery and or terminal connections have been responsible for many scenarios like you describe.

Re sensors, learn how to access DIAG system via the dash buttons and you can troubleshoot them from there. Other than a problem with the TPS many years ago, I think the sensors (and ECU) on the bike are actually very robust.

As the other guys said,check the battery terminals and if the valves in the cold start circuit are closed when the bike is warm.Also a defective TPS can cause this problem.The most times it works fine when you check it but the problem is there.Somewhere is a thread about the TPS..

Also there is an ECU recall for the 07,did it?

You said: ''The bike starts fine ad idles, until it warms to the 2-3 bar on the temp guage, then it will start to mis.''

This sounds like a very rich mixture..

Might want to verify that the "ground spider" recall was done properly. Here is the link to the repair notice. https://www-odi.nhtsa.dot.gov/acms/cs/jaxrs/download/doc/ACM18153811/RCRIT-11V338-2345.pdf

I would also find all the ground spiders and add electrical grease to them. this fixed a problem similar to this on my 2006 AE. I think I can dig up pictures on where they are if you can't.

Good luck.

Battery connections are clean and tight. I contacted Yamaha and no recall on this bike regarding the ECU. It did however have the wire recall performed.

The shop is also leaning toward the TPS.

Thanks for all the tips. About the "ground Spiders" are you refering to were the wires ground to the frame? How many are there?

Your sure you put gas in it?

I had a friend that thought he did but wasn't paying attention and never put more than a littl bit in the tank when he went to fill up. Hung the hose back on the pump and road off. Before long he was in trouble. It was only running on 2-3 cylinders for the next few miles, but he got it home. He was convinced it was bad gas because, of course, he just came from the gas station. Started fukin around with it to figure out what was wrong, only to find out he was out of gas.

Do check that cold start circuit as well. If that's not functioning correctly it will cause an over-rich fueling when the engine is warmed up.

Also,under of the gas tank in the front side under the t-bar there are many connectors.Unplug them and check if their terminals are not corroded and in good condition.Also spray some contact cleaner on the terminals.

Have reported many problems from those connectors.

Not sure but this problem sounds like it caused from a defective TPS or from an over rich mixture..

As about the ground spiders i am not an expert because i have a Gen 1.

Someone here with a Gen 2 where knows about,will help you soon i believe..

A malfunctioning cold start circuit will not cause a rich condition. At its basic function, the cold start circuit is no different than the idle speed adjustment, it is simply an air bypass circuit that lets additional air into the manifold. And like the idle speed circuit, the ECU has no direct input whether the cold start circuit is open or not. When open the ECU detects a lower manifold pressure and calculates the appropriate fuel to inject. A cold start circuit that doesn't fully close would cause a fast idle condition.

San Francisco. California bike, presumably. If so, yours has a charcoal canister/solenoid/etc. like my BMW did. Same circumstance- I stopped for gas. Hot day. Got back on bike, bike didn't run smoothly. Got worse, barely made it home. Bike wouldn't restart. Over thousands of miles of riding, my charcoal canister was full of charcoal dust, not rocks. Combine that with overzealous fillups leaving a little liquid gas overflow from time to time. By design, the emissions system captures overflow/fumes to reduce pollution to the atmosphere, then recovers fumes from the charcoal when there is a vacuum in the tank, using a solenoid and witchcraft. My (by then) powdered charcoal combined with fuel and became pudding. During my fuel stop, or just before it, vacuum in the tank resulted in the tank taking a sip from the canister. Instead of gas fumes, it sipped charcoal pudding, clogging and eventually welding the fuel filter shut. My kraut fuel pump refused to have its supremacy denied, and insisted on pumping until it blew its own crimp. Hope this isn't your problem.

70bsalightning said:

HI Guys, I want to put a question out here to see if someone else may have experienced the same issue I am having with my FJR.
2007 FJR1300AE

The bike has 29,000 miles and has always run flawlessly. Recently, I stopped to get fuel, at the same place I always get fuel, and within a few miles the bike started to sputter. Had sort of a mis to it. It didn't want to idle and at steady throttle, you could feel a hiccup where it used to be smooth.

It was due for service, so I took it to the shop for valve service and all the major work along with the diagnosis of my problem.

At first it semed to be just possibly some bad fuel. Drained the fuel and put in fresh from another source and the problem was still there.

Compression is good- same on all 4

Valves all within factory spec

New spark plugs

New air filter

Throttlebodies synced

And the problem still exists. there are no error codes thrown to the dash.

TPS is working according to the manual

The shop removed the fuel screws on each throttle body, found some gummy residue, cleaned each one and same problem.

Removed each injector- cleaned and blew through while open- same problem.

The bike starts fine ad idles, until it warms to the 2-3 bar on the temp guage, then it will start to mis.

The exhaust pipes are all a consistent temp to each other so it is hard to isolate if it is one particular cyl.

It will idle, but has a very prominent mis while idling, and if you rev, you can hear it missing as well.

Checked all the connections on the coils, they are tight, and all the spark plugs seem to be burning exactly the same.

I checked with Yamaha for any recalls and all have been performed on this bike.

We are leaning toward a sensor of some sort giving a bad signal, but shouldn't a bad sensor throw an error code?

How about a bad ECU? Has anyone ever experienced a bad ECU?

Thanks in advance guys, I am afraid the next step is to start changing parts out 1 at a time.

Click to expand...

When the bike is idling, there is a definite stumble that comes on and goes consistently. While this is happening, I disconnected the TPS and it stayed exactly the same. The only difference is you here a distict hissing sound when diconnected. I am not sure that is telling me anything or not. Part of me thinks that says the TPS is ok, and part says that means it is defective...... Any thoughts?

Use the DIAG feature to troubleshoot the TPS. Except for an intermittent connection issue, it should be a reliable method.

Sometimes the DIAG feature can not find the problem..

Denver & 70bcalightning have a look at this post :

https://www.fjrforum.com/forum//index.php/topic/164336-04-hesitating-stalling-in-very-hot-weather/?p=1247493

I can't find his original post..

Yep, another solid gold post from IONBeam!

Did you notice the methodical process he used (starting with DIAG) to isolate and then confirm the problem? I understand the difficulty of trying to troubleshoot a system that doesn't provide much feedback (hey Yamaha, how about an OBD interface?) but I detest "parts swapping" as a troubleshooting technique.

Many of the drive-ability issues that appear here the poster has already tried the basic stuff; TBS, tune-up, snake oil fuel treatment, etc and parts swapping is frequently the response posted to these issues. Hey, I get it. At this point it's going to require a deep-dive into the bike to determine root cause and many home mechanics and even some professional shops may not have the tools or time for this route.

Denver_FJR said:

...hey Yamaha, how about an OBD interface?...

Click to expand...

I have read that the Gen 3 has an OBD II port but so far nobody that has a Gen 3 has confirmed this. Until the port is sighted, pictured and documented it's another unicorn. If the Gen 3 has an OBD II port diagnostics just got much easier. It would (should) make it possible to also reset the '13 cruise control max speed to something realistic for the desert dwellers.

The Gen 3 is rumored to use a Mitsubishi FUA0010 ECU so the plug, codes and protocol should be Mitsubishi unless Yamaha had custom code written. Still, the basic code and structure has to be OBD II compliant. OBD-II diagnostics is a standardized data link connector and a set of standard SAE J/1979 defined Parameter IDs (PIDs). Vehicle manufacturers can have custom PIDs for their own vehicles and manufacturers don't have to support all modes. There are 10 categories for codes:

$01. Show current data

$02. Show freeze frame data

$03. Show stored Diagnostic Trouble Codes

$04. Clear Diagnostic Trouble Codes and stored values

$05. Test results, oxygen sensor monitoring (non CAN only)

$06. Test results, other component/system monitoring (Test results, oxygen sensor monitoring for CAN only)

$07. Show pending Diagnostic Trouble Codes (detected during current or last driving cycle)

$08. Control operation of on-board component/system

$09. Request vehicle information

$0A. Permanent DTC's (Cleared DTC's)

The $ is a software thingie that indicates the values are hexadecimal base, under each base code can be a long list of engine/vehicle function readings.

Yamaha has to play nice with some of the above code categories, though they may have other codes that are optional which a standard code reader couldn't handle.

Well ionbeam, you were totally on to something there and I just went ahead and replaced the TPS (because I'm running out of ideas) and unfortunately it did not solve the problem.

So I am back to the drawing board.

However, when the TPS was changed, I rode the bike when cold, as it seemed to be fixed at first start up, but then on the ride it started to stumble again as it got warmer. I decided to just ride it for a while to see if there was any consistency and at one point a quick flash of the engine light came on. So I tried to get it to do it again so I kept riding. No luck, but now it should have a stored error.

I checked and it shows a diagnostic code of 11

According to the FSM, the symptom is "No normal signals are received from the cylinder identification sensor"

The problem or malfunctions:

- Open or short circuit in sub wire harness

- Open or short circuit in wire harness

- Defective cylinder identification sensor

- Malfunction in ECU

- Improperly installed cylinder identification sensor

So now I have since cleared the error and tried to get it to come on again and have had no luck.

And there seems to be no consistency when it decides to run poorly. At one point it was completely warm and it cleared up and was fine, but soon came back to poor.

70bsalightning said:

...
So now I have since cleared the error and tried to get it to come on again and have had no luck.

And there seems to be no consistency when it decides to run poorly. At one point it was completely warm and it cleared up and was fine, but soon came back to poor.

Click to expand...

The ECU isn't consistent when it will throw a code so I wouldn't wait for code to reappear. It's possible to disconnect some sensors without any code reported by the ECU.

The code 11 you received is the best indication of fault I've heard so far. Why not troubleshoot it? See the steps listed in "Checking the Cylinder Identification Sensor".