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  1. #1

    2006 Yamaha Waverunner stalls on idle (please help)

    I have done everything I can to try and diagnose this issue. 2006 Waverunner FX/HO 1100, 275 Hours, stalls when idle. Seems to run perfectly fine when hooked up to the hose, no rough idle (or not nearly as rough) as when put in the water. I replaced plugs, checked the gap on the plugs, compression readings floating around 223 on all 4 however cylinder 1 SLIGHTLY less but certainly not drastic enough to where I think it would be an issue. Cleaned the carbs, treated the fuel, took the fuel pump out and checked and cleaned the filter at the bottom of the pump housing, no major blockage, little sand nothing crazy, brand new air filter, oil filter and oil. I have no performance issues at full throttle but slightly struggles out the gate. Once I release the throttle, it eventually starts to rough idle within about 5 seconds and then usually stalls 25-30 seconds later...not everytime, but most times. WHAT GIVES????? PLEASE help.


  2. #2
    powerstroke specialist mikegp's Avatar
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    this is what happen to me , the throttle bodys somehow got out of synchronization , it was exactly like yours , Yamaha did cover that issue under the warranty, unfortunately the Yamaha dealer here did such a bad job that I ended getting the tool from a friend that has a bike shop and take care it myself. its real simple to do the head has one port under the bodys each cylinder has its own port. you will need the vacuum tool that has 4 gauges . you can get them on eBay.
    after I did the synch job it idle perfectly. no more problems .keep in mind this was my problem , doesn't mean yours will have the same issue. it was just my experience.

  3. #3
    powerstroke specialist mikegp's Avatar
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    this what you will need to do the job . remember you will need the 6mm adapters for Yamaha.
    http://www.ebay.com/itm/MOTION-PRO-S...7e911f&vxp=mtr

  4. #4
    Quote Originally Posted by mikegp View Post
    this is what happen to me , the throttle bodys somehow got out of synchronization , it was exactly like yours , Yamaha did cover that issue under the warranty, unfortunately the Yamaha dealer here did such a bad job that I ended getting the tool from a friend that has a bike shop and take care it myself. its real simple to do the head has one port under the bodys each cylinder has its own port. you will need the vacuum tool that has 4 gauges . you can get them on eBay.
    after I did the synch job it idle perfectly. no more problems .keep in mind this was my problem , doesn't mean yours will have the same issue. it was just my experience.
    I hate to be THAT guy but can you be a little bit more descriptive as to how to go about performing this adjustment? Thanks in advance.

  5. #5
    r33pwrd's Avatar
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    Quote Originally Posted by RyanPuckhaber View Post
    Quote Originally Posted by mikegp View Post
    this is what happen to me , the throttle bodys somehow got out of synchronization , it was exactly like yours , Yamaha did cover that issue under the warranty, unfortunately the Yamaha dealer here did such a bad job that I ended getting the tool from a friend that has a bike shop and take care it myself. its real simple to do the head has one port under the bodys each cylinder has its own port. you will need the vacuum tool that has 4 gauges . you can get them on eBay.
    after I did the synch job it idle perfectly. no more problems .keep in mind this was my problem , doesn't mean yours will have the same issue. it was just my experience.
    I hate to be THAT guy but can you be a little bit more descriptive as to how to go about performing this adjustment? Thanks in advance.
    you have any buddies that ride bikes (If so they could probably help you)? I have done them on cars and a bike and they are not hard but it does take some work.

  6. #6
    powerstroke specialist mikegp's Avatar
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    Quote Originally Posted by RyanPuckhaber View Post
    Quote Originally Posted by mikegp View Post
    this is what happen to me , the throttle bodys somehow got out of synchronization , it was exactly like yours , Yamaha did cover that issue under the warranty, unfortunately the Yamaha dealer here did such a bad job that I ended getting the tool from a friend that has a bike shop and take care it myself. its real simple to do the head has one port under the bodys each cylinder has its own port. you will need the vacuum tool that has 4 gauges . you can get them on eBay.
    after I did the synch job it idle perfectly. no more problems .keep in mind this was my problem , doesn't mean yours will have the same issue. it was just my experience.
    I hate to be THAT guy but can you be a little bit more descriptive as to how to go about performing this adjustment? Thanks in advance.
    you will need to remove the air cleaner completed and reinstall your throttle bodys w/o the air cleaner once you do that you will be able to access the vacuum ports under the throttle bodys, there is one port for each cylinder, once you discover the port install the 6mm adapter that comes with the kit, install hoses make sure not to cross them ,that way you will know for sure witch cylinder are you doing the adjustment . once you have all that connected you will need to have the engine running and water hose connected, let it get normal operation temperature, you will be able to feel the hot water coming off the back . at that point you need to check the gauges and see witch one will need adjustment.
    YOU WILL NEED THE SERVICE MANUAL TO DO THIS. IT WILL EXPLAIN IN DETAILS HOW TO PERFORM IT .

  7. #7
    Quote Originally Posted by RyanPuckhaber View Post
    I have done everything I can to try and diagnose this issue. 2006 Waverunner FX/HO 1100, 275 Hours, stalls when idle. Seems to run perfectly fine when hooked up to the hose, no rough idle (or not nearly as rough) as when put in the water. I replaced plugs, checked the gap on the plugs, compression readings floating around 223 on all 4 however cylinder 1 SLIGHTLY less but certainly not drastic enough to where I think it would be an issue. Cleaned the carbs, treated the fuel, took the fuel pump out and checked and cleaned the filter at the bottom of the pump housing, no major blockage, little sand nothing crazy, brand new air filter, oil filter and oil. I have no performance issues at full throttle but slightly struggles out the gate. Once I release the throttle, it eventually starts to rough idle within about 5 seconds and then usually stalls 25-30 seconds later...not everytime, but most times. WHAT GIVES????? PLEASE help.
    A little more info if possible. Has the ski been sitting for a while? Did this problem just pop up? When was the last time it ran properly. You say you treated the fuel, does this mean the fuel in your tank has been there for a while. If so, whether treated or not, drain it and start with fresh fuel.

  8. #8
    Quote Originally Posted by slingshot View Post
    Quote Originally Posted by RyanPuckhaber View Post
    I have done everything I can to try and diagnose this issue. 2006 Waverunner FX/HO 1100, 275 Hours, stalls when idle. Seems to run perfectly fine when hooked up to the hose, no rough idle (or not nearly as rough) as when put in the water. I replaced plugs, checked the gap on the plugs, compression readings floating around 223 on all 4 however cylinder 1 SLIGHTLY less but certainly not drastic enough to where I think it would be an issue. Cleaned the carbs, treated the fuel, took the fuel pump out and checked and cleaned the filter at the bottom of the pump housing, no major blockage, little sand nothing crazy, brand new air filter, oil filter and oil. I have no performance issues at full throttle but slightly struggles out the gate. Once I release the throttle, it eventually starts to rough idle within about 5 seconds and then usually stalls 25-30 seconds later...not everytime, but most times. WHAT GIVES????? PLEASE help.
    A little more info if possible. Has the ski been sitting for a while? Did this problem just pop up? When was the last time it ran properly. You say you treated the fuel, does this mean the fuel in your tank has been there for a while. If so, whether treated or not, drain it and start with fresh fuel.
    So I didn't mention this thinking it wasn't worth mentioning but after bringing it to the "experts" at a local Yamaha waverunner dealer...his best diagnosis he came up with is the fact that I didn't bolt in the spark plug coils and rather set them in firmly, thinking the grab from the rubber on the spark plug itself was enough where not bolting the coils in would be a problem. THIS, to me seems extremely far fetched but I want a second opinion if you can help....thanks again btw, according to the "expert" it purs like a kitten on land yet on water is where it stalls

  9. #9

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    why didn't you bolt them? if it doesn't turn out to be the issue why not bolt them back?
    Check the idle control valve. That would be the first thing I check after plugs. You need to have the shop manual for this. It has the acceptable range. or Yamaha dealer can connect their YDS software to it and read it.

  10. #10
    powerstroke specialist mikegp's Avatar
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    Quote Originally Posted by CaptainReza View Post
    why didn't you bolt them? if it doesn't turn out to be the issue why not bolt them back?
    Check the idle control valve. That would be the first thing I check after plugs. You need to have the shop manual for this. It has the acceptable range. or Yamaha dealer can connect their YDS software to it and read it.
    I will assumed if he has a bad idle control motor it will display a code . Unless he has a broken vacuum hose.

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