Engine only runs with vacuum line disconnected

[Zpetrus]

Hello All,
I aquired a 2005 fjr that has not run since 2006. 4,900 miles. After kicking out the mice and cleaning her up and looking at the wiring harness for damage - minimal
I replaced:
Battery
fuel pump
fuel injectors
air filter
spark plugs
oil
cleaned out gas tank & lines and fuel rail - throttle bodies looked clean - boots to rail & bodies look good
new gas
now the engine turns over fine and "pops" while the starter is engaged and stops when the starter stops.
Runs on starter fluid. Strong spark on all cylinders
Started looking harder at the vacuum lines and found that the engine starts, runs, and revs (though a bit not rough, but not smooth) with the vacuum line disconnected from the fuel pressure regulator. It stops running if I reconnect the vacuum line or plug it with my finger. I now have an intermittent check engine code 16. Intake air pressure sensor, atmospheric pressure sensor, throttle position sensor. Do any of you more experienced folks know where I might start looking for a fault and how to check these components without just throwing parts at it? Why would an obvious vacuum leak allow the engine to run? It does not seem to matter where a vacuum line is disconnected (within reason). Any insight would be appreciated. Thanks in advance.

 

[RossKean]

Bad Pressure Sensor (MAP)?
#18 here
https://www.partzilla.com/catalog/yamaha/motorcycle/2005/fjr1300-fjr13t/intake-2
Atmospheric pressure sensor(s) have been responsible for running issues in Gen II bikes (Probably Gen I as well) although it generally induced a #14 fault code in the Gen II.
Check this thread
https://www.fjrforum.com/threads/fault-code-14-gen-ii-solved.170314/
Worth checking all of the hoses and fittings connected to the sensor and regulator to make sure none is plugged or cracked.
Engine will run like crap (if at all) if that sensor is buggered in some fashion.

 

[road runner]

Sounds like it needs more fuel to run. By unhooking a vacuum line anywhere, the MAP sensor see's low vacuum and thinks the engine is at WOT, so it tells the ECM to richen it up by holding the injectors open longer. Test this by just taking the vacuum line off the MAP sensor and see if it runs. Then plug the line and it should still run if it's related to the MAP and running lean.

Don't know yet but something to try. This will just tell if it wants more fuel.

 

[Zpetrus]

Thanks RR for the insight / suggestion. I did the test - reconnected the vacuum line to the pressure regulator and disconnected the vacuum line to the pressure sensor, blocking off the removed line. The engine started, ran, and revved as before with just the vacuum line to the regulator removed. Does that mean that the pressure sensor (MAP) is bad? I pulled a spark plug and it appeared wet and black (new plug yesterday) see photo. Am I correct in assuming that this is what would be predicted by running the engine with a vacuum line open?

 

[RossKean]

Don't put too much stock in the appearance of a plug. Unless you ran the engine until it had warmed up and came off fast idle, I would expect it to be dark.

Before you consider replacing the pressure sensor, check its electrical connections, the orifice where the rubber tube connects as well as all of the associated plumbing, hoses and connectors for blockage and cracks. The lines and connectors can be spritzed with a suitable solvent (and dried before reconnection). I used a metal rod through the hoses after removing them followed by a pipe cleaner and then some solvent - carb cleaner IIRC. Note: Carb cleaner may damage plastic bits and cause rubber to swell if in contact too long. Mineral spirits might be a better idea although they take longer to evaporate. Don't put anything (solvent or implement to attempt to clean it out) into the sensor itself.

Make sure that the throttle synch caps are all present and accounted for but I doubt a missing or cracked cap would have this much effect.

Not saying it is the sensor, but it seems to be a significant possibility. Are there any stored error codes?

 

[Zpetrus]

Error code 16, which indicates TPS, MAP, and another pressure sensor.

 

[RossKean]

Error code 16, which indicates TPS, MAP, and another pressure sensor.

Clean the stuff up and go from there. What is the other pressure sensor?
TPS has been known to go bad on Gen I but not to the point where it prevents any running. Have you done any of the diagnostics for the TPS?
The pressure sensor I referenced in my first post (or associated electrical connections/hoses/plastic connectors) seems to me to be most probable...

Edit: I just reread your original post and it clicked that the the bike only has 4900 miles! Also that it hasn't run in 16 years!
Makes it more likely to be electrical in nature. I would check, clean and use dielectric grease on every connector. There is one that has been problematic on some Gen I - big white connector under the tank:
https://www.fjrforum.com/threads/main-ecu-connector-contamination.22734/Have a close look at the connector (and wiring) that goes to the ECU as well.

Still very much worthwhile looking at the pressure sensor stuff. Blockage or crack in that system will cause problems (as will a bad sensor).
TPS seems less likely. Although there were some failures in Gen I, I believe they were wear related. Not likely at 4900 miles unless moisture got in. Bike diagnostics should be able to eliminate the TPS - at least I know you can verify on Gen II.

Hope there isn't hidden rodent damage!

 

[Zpetrus]

I stripped the bike down to it's engine frame. The mouse wire damage is astonishing minimal. Looked for that first. I will look into the Vacuum lines tomorrow while the brisket slow cooks - never thought they could be clogged, just breached.

 

[torch]

Instead of just guessing, have a look at the actual values reported to the ECU by the sensors in Diag mode.

01 - Throttle angle. Closed = ~16, Open = ~99. Verify that the value changes smoothly with throttle operation. Fail safe = WOT

02 - Atmospheric pressure in mmHg. Verify against current actual A.P. by barometer. Fail safe = 760mmHg

03 - Pressure difference (A.P. - intake air pressure in mmHg). Should be about 0 with engine off. Generate a difference by cranking with starter motor without starting engine. Block intake with hand for maximum difference. Should be 10 - 200 mmHg. Fail safe = 0

05 - Intake Air temp. -- temp inside air case. Around ambient if engine has not been run. (I think temps are given in °C, even in US bikes). Fail safe = 20°C.

06 - Coolant temp -- should be around ambient if the engine has not been run. Fail safe = 60°C.

Personally, I would be more suspicious of temperature error(s) in this case. If the ECU thinks it's -20° when it is actually +20°C, it will over-fuel the engine. This could explain why it runs when introducing a vacuum leak.

If in doubt, unplug the sensor(s) to put things in fail-safe mode. The engine can run with any or all of the above sensors unplugged.

Fuel pressure: If the sensors all check out, then you may have a fuel pressure issue. The regulator decreases fuel pressure with increasing vacuum. Pressure is at max with the engine off, minimum at idle or closed throttle decel, somewhere in between during accel. Since your problem is in the starting of the bike, when the fuel pressure is at max anyway, disconnecting the vacuum line has no bearing on the problem from a regulator standpoint. That said, the pressure may provide clues to other possible issues.

Note that black sooty plugs are an indicator of incomplete combustion not a reliable indicator of rich/lean. Obviously, a rich condition generally results in incomplete combustion, but so can a lean condition. If the mix is too lean to fire reliably, the fuel builds up until it is rich enough so the cylinder "pops" -- inefficiently burning some of the excess fuel and blackening the plugs.

To check fuel pressure properly, you need a pressure gauge inserted in the line to the injectors (quick connect on left side). To check regulator properly, you need a vacuum pump such as a Mity Vac, but since this is a starting issue, that is not necessary right now. Install the gauge, run the fuel pump and check that pressure climbs to ~250Kpa/36psi and holds.

If the pressure plummets immediately, you have probably have one or more leaking injectors flooding the engine. It might start and run on starting fluid (or propane) as the combustible range is much broader than the combustible range of gasoline so the starter fluid can burn even when the gasoline cannot.

Disconnect the injector electrical connectors, remove the injector bank, lay on an absorbent pad, pressurize the fuel rail temporarily and visually confirm which injector(s) are leaking. NOTE: LEAKING INJECTORS WILL SPRAY HIGHLY FLAMMABLE GASOLINE! USE EXTREME CAUTION IN A SAFE, WELL VENTILATED ATMOSPHERE! (Preferably outside, with a fire extinguisher handy). ENSURE ENGINE STOP SWITCH IS SET TO "OFF". Wear safety GOGGLES.

Conversely, you may have one or more plugged/stuck closed injectors. With the fuel gauge installed and rail pressurized but pump disconnected, injectors can be manually actuated by toggling the run switch from off to on in Diag mode 36 through 39. 36 = injector 1, 37 =2, etc. The injector should pulse 5 times and you should see a corresponding drop in fuel pressure as the injector fires. Reconnect the fuel pump and repressurize between injectors.

If you don't have access to a fuel pressure gauge, you can do a down-and-dirty check by removing the injectors as above, connecting the electrics and manually firing the injectors in Diag. It's not a guarantee, but if you get a decent spray pattern that shuts off completely from each injector, it at least confirms that you have some fuel pressure and the injectors are functional.

If any one injector does not fire, a noid light is recommended to verify the electrical signal is being delivered. But a down-and-dirty alternative is to swap the connector with a known good injector and recheck. If the problem moves, then the problem is electrical. If the same injector won't fire, the problem is the injector.

Spark: I doubt this is the problem, since it runs on starter spray. That said, you may need too replace those new plugs again once you find and correct the underlying problem. Black plugs often cause misfires. Sometimes you can "burn the carbon off" but personally I've never found a carboned plug that worked properly thereafter. Once the carbon build-up reaches a certain level, there's no bringing them back. IMHO.

 

[road runner]

Thanks RR for the insight / suggestion. I did the test - reconnected the vacuum line to the pressure regulator and disconnected the vacuum line to the pressure sensor, blocking off the removed line. The engine started, ran, and revved as before with just the vacuum line to the regulator removed. Does that mean that the pressure sensor (MAP) is bad? I pulled a spark plug and it appeared wet and black (new plug yesterday) see photo. Am I correct in assuming that this is what would be predicted by running the engine with a vacuum line open?

If it starts and runs after unplugging the MAP and plugging the Vacuum line, then that tells me the MAP is working. Because you plugged the line you are not introducing air and leaning it out. When the MAP has no vacuum it tells the ECM max load or WOT so the ECM richens things up by keeping injectors open longer. If you did this test and nothing was different then I would say the MAP may be bad, but because is richens it up and then starts and runs that means it is working as designed. Also a good idea to check all vacuum lines for leaks or plugs, but from what you said the engine did when you removed and or plugged them up, it sounds like they are all working.

Now you have to figure out why it needs to be richened up so much to start and run. Like others said I would go to diag. screen to see what the ECM is seeing from all the sensors. Clear fault codes and see if any come back. The code in it may be an old code. Also Need to check fuel pressure. Low pressure will make it lean. A leaking injector will make one cylinder too rich but other 3 cylinders lean. Put a pressure gage on it, key up and make sure pressure is good, key off and make sure it stays for long time. If pressure drops off right away that says leaking injector.

 

[RossKean]

My money is still on the pressure sensor (and associated plumbing) or a corroded electrical connection (we will assume rodent damage has been dealt with) BUT I like Torch's far more systematic approach. Stuff you can do via the diagnostic function is "low hanging fruit" - easy, non-invasive stuff that could reveal a smoking gun in just a few minutes. Something as simple as a temperature sensor might make all the difference. Checking sensors via a diagnostic rather than a meter (resistance or voltage) is useful because this is what the ECU "sees". If something is amiss, you find out whether it is the sensor or a connection back to the ECU. I found that when I had an issue with an O2 sensor, the bike ran very poorly with the sensor connected (it was producing the WRONG information) but OK with it disconnected - as Torch mentioned, the "fail-safe" result may help with the ultimate diagnosis.
Note: The O2 sensor issue did not produce any diagnostic anomaly but sure made it run horribly. Wire was crushed between the timing cover and the case resulting in a partial (and variable) connection to ground. Happened when replacing the CCT.

In case you don't have the Diagnostic Code information, ionbeam posted a nice reference for both Gen I and Gen II:
https://www.fjrforum.com/threads/diagnostic-codes.9612/Worth going through everything for the little time it takes.

While TPS, injectors and pressure regulator are not likely based upon the extremely low mileage, anything might happen with the 16 years of inactivity! Injectors, in particular, are susceptible to plugging (the OP mentioned that they had already been replaced but I wouldn't entirely dismiss the possibility of a problem). Personally, I haven't heard of an FJR fuel pressure regulator failure but anything can happen over that much time. With a new fuel pump (replaced by OP), it seems likely that sufficient fuel pressure is being supplied but still may not be regulated correctly.

Good luck and let us know what works (and what doesn't).

 

[Zpetrus]

First, Thank you all for the input. It is much appreciated.
I took off all the vacuum lines attached around the fuel rail and cleaned and inspected - no leaks or blockage.
Regarding Torch's diagnostics:
01 throttle position sensor - bike read 16 - 100 closed to open and moves smoothly
02 Atmos pressure - bike read 97 - barometer 29.91 inHg, 759.81 mmHg Huge difference here or is the decimal place off on the bike?
03 Pressure Difference - Engine off = 0 Engine turning on starter motor with my hand over air intake = 7
05 Intake air temp - Bike read 35 Ambient 30C
06 Coolant temp - Bike read 34 Ambient 30C (note my thermometer may not be the most accurate)

I have not done the fuel pressure tests as it looks like #02 and #03 readings are way off. I did the test on 8-57 of the shop manual. The voltage across the blue and black blue lines reads 5.2 with the key on. Spec is 3.75-4.25 Does this indicate that the sensor is bad? Can I do further tests to check these units. Now the bike is showing a check engine code of 14 instead of 16 which was the earlier fault Both have to do with the pressure sensor. I did not check the one under the seat. A bit of work to get to.
Ideas

 

[RossKean]

Do we assume measurement is supposed to be in mm? If either mm or in of Hg, it is way off. Pretty close if it is supposed to be a percent of normal atmosphericpressure... I have no idea and no point in me checking my Canadian Gen II.

If it is wrong, is it the sensor or the connection back to the ECU? Did you look at the condition of the big connector under the tank? What about the ECU connector?

Have a look inside the sensor with a bright light and make sure there isn't a glob of goo there. I wonder what would happen if you tried starting with the sensor disconected electrically...?

I think you have to check the other pressure sensor and connections as well and see if someone can get back to you on the pressure units and expected readings for a US Gen I.

I would make sure this stuff is right before going further. Did you go through the other diagnostic stuff that can be done?

 

[road runner]

All of your readings look normal. I don't think the Baro ready is not inches or mm of Hg. I think it is just a number sent to ECM that changes with baro then the ECM looks at a chart to come up with the proper settings. I'm pretty sure about this but not certain so it needs to be checked.

Did you erase the old fault codes (after you document them) then see what new ones come back?

I still think it is too lean. Things that affect the mixture the most are Air and coolant temp sensors, MAP sensor, FP regulator, and fuel pressure.

You could try unhooking the MAP and temp sensors and see if it runs better. That should put it in limp home mode. If that does not do it then you need to check fuel pressure (FP). You may have a stuck injector.

I'm not familiar with the Gen1 fuel system. I think it has a 2 fuel lines or a return. My Gen 2 has one fuel line. If it has a return, you could try pinching the return to restrict it and raise the FP. See if you can act like a FP regulator. I have done this on other things, but you should have a FP gage on it so you can see what is going on.

Just some ideas. I'm not a Yamaha FJR tech, but I did stay at a Holiday Inn Express once. lol.

 

[road runner]

Do we assume measurement is supposed to be in mm? If either mm or in of Hg, it is way off. Pretty close if it is supposed to be a percent of normal atmosphericpressure... I have no idea and no point in me checking my Canadian Gen II.

If it is wrong, is it the sensor or the connection back to the ECU? Did you look at the condition of the big connector under the tank? What about the ECU connector?

Have a look inside the sensor with a bright light and make sure there isn't a glob of goo there. I wonder what would happen if you tried starting with the sensor disconected electrically...?

I think you have to check the other pressure sensor and connections as well and see if someone can get back to you on the pressure units and expected readings for a US Gen I.

I would make sure this stuff is right before going further. Did you go through the other diagnostic stuff that can be done?

Also as Ross mentioned. The big white wire harness plug under the tank towards the front. It has been known to cause running issues if there's any corroded connectors in it.

 

[Zpetrus]

Thank you again for the input. Interestingly, as both Torch and Roadrunner suggested, I tried disconnecting the wires to the Pressure sensor located the fuel rail and no improvement - still no start - however with it connected it ran when I introduced the vacuum leak at the fuel pressure regulator (disconnected that line) and the bike would start and rev with pressure sensor disconnected it would not run. I am thinking it is this sensor as it is out of spec and the diagnostic on the bike keeps pointing to it. Also a new observation - when I disconnect the fuel line gas flows freely which I think I read somewhere that only that which was in the line would leak. Is this true or is it possible when I replaced the fuel pump an o-ring did not seat or something?
Again I did clean and check all the vacuum lines for leaks. I did check all the wiring harness for breaks and the connectors for corrosion when I kicked the mice out.

 

[torch]

My Canadian 03 reads 734 this morning with an actual atmospheric pressure of 767mmHg, so I'm pretty sure it's in mmHg. That said, it should not be critical to engine operation -- it was deleted in the Gen II models.

What is the Diag value if you check with the AP sensor unplugged? Does it revert to the fail-safe value? If it reverts to fail-safe and sets a fault code 23, then I think that points to a fault in the sensor. If unplugging the sensor has no effect, then I think it points to wiring. The AP sensor is used to calculate mixture compensation, particularly for high altitudes. With a value of 97, the bike probably thinks it's sitting on top of Mount Everest.

The tests shown in the manual for the pressure sensors do not state this specifically, but I believe they are to be done by back-probing the connector (as shown on page 8-3) with the sensor still connected. When you measured the voltage was that with the sensor connected or across the unplugged connector?

Most of the sensors share a common logic high and low. Probably 5 volts or so. The ECU looks for the variance from 5 volts on the third wire to each sensor. So if you unplug the sensor and measure the potential across the connector, you are just reading what the ECU is supplying to the sensor, not what the sensor is reporting back to the ECU. Your measurement of 5.2 volts sounds like the sensor is unplugged during the test, or defective, or there's a problem with the wiring between sensor and ECU.

Code 14 may have been caused by the intake air pressure sensor if you unplugged it for the test above, although that should be accompanied by a code 13. (Are you checking for multiple history codes in Diag 61?) I would clear it and see if it comes back. However, it could be related to the throttle position sensor. The system compares TPS operation against IAP. If the TPS is changing but the IAP is not, this might set a 14.

Code 16 is very similar. The system thinks the TPS is stuck because it is not changing in relation to the IAP. Could be caused by a fault in the sensors or the wiring.

 

[Zpetrus]

My Canadian 03 reads 734 this morning with an actual atmospheric pressure of 767mmHg, so I'm pretty sure it's in mmHg. That said, it should not be critical to engine operation -- it was deleted in the Gen II models.

What is the Diag value if you check with the AP sensor unplugged? Does it revert to the fail-safe value? If it reverts to fail-safe and sets a fault code 23, then I think that points to a fault in the sensor. If unplugging the sensor has no effect, then I think it points to wiring. The AP sensor is used to calculate mixture compensation, particularly for high altitudes. With a value of 97, the bike probably thinks it's sitting on top of Mount Everest.

The tests shown in the manual for the pressure sensors do not state this specifically, but I believe they are to be done by back-probing the connector (as shown on page 8-3) with the sensor still connected. When you measured the voltage was that with the sensor connected or across the unplugged connector?

Most of the sensors share a common logic high and low. Probably 5 volts or so. The ECU looks for the variance from 5 volts on the third wire to each sensor. So if you unplug the sensor and measure the potential across the connector, you are just reading what the ECU is supplying to the sensor, not what the sensor is reporting back to the ECU. Your measurement of 5.2 volts sounds like the sensor is unplugged during the test, or defective, or there's a problem with the wiring between sensor and ECU.

Code 14 may have been caused by the intake air pressure sensor if you unplugged it for the test above, although that should be accompanied by a code 13. (Are you checking for multiple history codes in Diag 61?) I would clear it and see if it comes back. However, it could be related to the throttle position sensor. The system compares TPS operation against IAP. If the TPS is changing but the IAP is not, this might set a 14.

Code 16 is very similar. The system thinks the TPS is stuck because it is not changing in relation to the IAP. Could be caused by a fault in the sensors or the wiring.

I did the test on 8-57 of the shop manual for the intake air pressure sensor. The voltage across the blue and black blue lines reads 5.2 with the key on. Spec is 3.75-4.25 I suspect this indicates that the sensor is bad. This was done with lead wires maintaining connections to the bike and testing across them with the ignition on as per the manual. Now the bike is showing a check engine code of 14 instead of 16 which was the earlier fault Both have to do with the pressure sensor. I did not check the one under the seat. A bit of work to get to.

Regarding the TPS I ran the diagnostic and it is within spec and working smoothly. Unless you think it is possible that the Diagnostic is wrong and reading something different than the ECU.

Interestingly, if I unplug the intake air pressure sensor the bike will not start at all - vacuum line connected or disconnected.

I am going to do the disassembly required to get to the APS today perhaps if it is disconnected it will solve the issue since it is way off and the default is closer to what exists here.

Again, Thanks for the pointers Torch

 

[torch]

The values displayed in Diag mode come from the ECU and therefore indicate what it is seeing. So the TPS readings are good.

That's why I think unplugging the AP sensor should result in a Diag display of 760 if the problem is with the sensor -- the ECU should display the value it is using and the value should be set to the fail-safe if the sensor is disconnected.

 

[Zpetrus]

I disconnected the APS sensor and the bike is a no start with or without the forced vacuum leak at the fuel regulator. Diagnostics read 120 - still pretty far from the actual atmospheric pressure.
I tried connecting all sensors and moving the vacuum leak to the TPS. Bike starts, but runs worse that when the line is disconnected at the fuel regulator. The check engine code is back to 16 after all the juggling.