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Hello everyone! I have a issue with my 2006 ninja 650r. A little backstory i bought this bike with 26k miles last year and before that it sat outside uncovered for 3 years. As of right now it sometimes runs on one cylinder, it seems to happen at idle and then will kick in at higher speeds after some stuttering and sputtering. Or sometimes it runs on one cylinder for miles before it comes to life. Then goes back to one cylinder usually at idle or at low rpms. It also seems to sputter and stutter at higher throttle when both cylinders are working. At one point after replacing the gas tank and fuel pump it ran for about 3000miles perfectly then i noticed it stuttering at high rpms then it died on me once then it died and wouldnt start and it got put away for the winter, this spring we found one of the coils was loose and it started up and seemed to run just fine until my clutch cable broke and I drove it home in first gear then it sat for another two weeks until the cable came in then it really started acting up.
This is what i have done to it so far,
Gas tank(Old one was rusted badly)
Fuel pump
Injectors
Coils
Spark plugs(cylinder 1 plug was rich/black and 2 was lean/white)
generator and rectifier
Battery

Ive ran all kinds of cleaning agents through the system, also the bike has a power comander with a two brothers exhaust with the proper map on it.
as far as i can tell the coils and plugs are working properly and getting proper voltage. At this point i dont know what else to do besides bring it to a professional but feel almost defeated by this **** cursed bike haha.
 

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I have a 2007 Kawasaki 650i Ninja one cylinder not running when you get up to speed a little bit of spiders kicks in and runs for a little bit and then stops when you slow down .what's wrong with it.
 

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I have a 2007 Kawasaki 650i Ninja one cylinder not running when you get up to speed a little bit of spiders kicks in and runs for a little bit and then stops when you slow down .what's wrong with it.
Hi welcome to the forum, first thoughts would be , Spark Plug , Stick Coil or Injector, have you identified which cylinder , maybe a temperature gun on the down pipes might show up the culprit,
Oh and dirty fuel pump
 

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Hi welcome to the forum, first thoughts would be , Spark Plug , Stick Coil or Injector, have you identified which cylinder , maybe a temperature gun on the down pipes might show up the culprit,
Oh and dirty fuel pump
I replace all those parts and the only things I haven't replace is stator regulator and rectifier and ignition. Check wiring can't find anything bad I have no testers to test electrical.
 

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I replace all those parts and the only things I haven't replace is stator regulator and rectifier and ignition. Check wiring can't find anything bad I have no testers to test electrical.
Also replace the fuel injectors throttle body and fuel pump.I am 62 years old on social security and need all the help I can get. I have done all the work on this bike myself but I am limited as to what I can do. It is the number two cylinder.
 

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When you pulled the spark plugs out, what did they look like? Was there any difference between plug#1 and plug#2?
 

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Have you done the valve clearances , with only one cylinder acting up it might be out of spec
 

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Ok, but neither spark plug looked black or oily, correct? Was the rich plug the one in the cylinder that you are having trouble with?

I would do a compression check and if compression is down then do a wet compression check. A wet check is done by adding a teaspoon of oil to the cylinder and then running the compression test again. If the oil made a difference then you know you have leakage past the piston rings. If the wet check made no difference then I would check the valve clearances as suggested by Ropp.

Also are you using a good quality fuel with high octane and preferably without ethanol? I would try draining the tank, refilling with good quality fuel and adding in your favourite injector cleaner. I like to use Seafoam but there are many products on the market.
 

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Ok, but neither spark plug looked black or oily, correct? Was the rich plug the one in the cylinder that you are having trouble with?

I would do a compression check and if compression is down then do a wet compression check. A wet check is done by adding a teaspoon of oil to the cylinder and then running the compression test again. If the oil made a difference then you know you have leakage past the piston rings. If the wet check made no difference then I would check the valve clearances as suggested by Ropp.

Also are you using a good quality fuel with high octane and preferably without ethanol? I would try draining the tank, refilling with good quality fuel and adding in your favourite injector cleaner. I like to use Seafoam but there are many products on the market.
I have change fuel and run several tanks of gas with Gumout injector carburetor cleaner. Valves are open and closing had recent tune up.
 

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Ok
Ok, but neither spark plug looked black or oily, correct? Was the rich plug the one in the cylinder that you are having trouble with?

I would do a compression check and if compression is down then do a wet compression check. A wet check is done by adding a teaspoon of oil to the cylinder and then running the compression test again. If the oil made a difference then you know you have leakage past the piston rings. If the wet check made no difference then I would check the valve clearances as suggested by Ropp.

Also are you using a good quality fuel with high octane and preferably without ethanol? I would try draining the tank, refilling with good quality fuel and adding in your favourite injector cleaner. I like to use Seafoam but there are many products on the market.
I have done fuel change with shell gas and fuel injection cleaner. The spark seems weak to me when I turned the engine over with the spark plugs against the frame I could see the spark but it seemed weak.The bike doesn't smoke or burn oil. The bike has 20,000 mi on it. I have not checked vale clearance.Was in the Kawasaki shop had tune up done to it. They said it was a good little running bike until this recent shutting down of one cylinder.
 

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Have you had a vacuum sync done?
Know I haven't. I haven't had a diagnostic test done on it either I don't have the code reader. There are so many things to check with these fuel injection bikes.I am old school used to the old Kawasaki 1000s and drag racing in the 80s with carbureted bike. Not really used to these fuel injected bikes but I'm trying to learn. The biggest thing is I don't have a place to work on the bike it's getting cold and I don't have the testers to test anything and the shops just eat up money trying to figure out what's wrong with it.
 

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Ok good work! We are getting some good information here and you have checked off a lot of the boxes. Shell fuel and injector cleaner is an excellent start. Weak spark is very interesting. Was it weak on both cylinders? If not swap the spark plugs to see if it makes a difference.

Earlier you said you replaced spark plugs and coils. Were they new or used?
 

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I hear you about getting cold with no place to work where it is warm. I am from Canada so I know all about cold.
Hey, if you have to shut this project down until Spring that's ok. We will still be here. Or if a warm day comes along, keep at 'er.
 

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Ok good work! We are getting some good information here and you have checked off a lot of the boxes. Shell fuel and injector cleaner is an excellent start. Weak spark is very interesting. Was it weak on both cylinders? If not swap the spark plugs to see if it makes a difference.

Earlier you said you replaced spark plugs and coils. Were they new or used?
They were new spark plugs and coil sticks.swap pugs and replace plugs .No change.
 

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Take a look at this matey, can make your own synchroniser or hire one to balance, on page 2-15 of the manual, do you have the manual?
 
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