Surging, Sputtering at 4,000-5,000 RPM

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Any stored fault codes?
TPS failure not common for Gen II. More in Gen I and III+ but still possible. Just because you hear the FI pintel "fire", it doesn't necessarily mean that the injector isn't partly plugged.
 
NO Stored fault codes. The missing is not just in one spot its from idle up to the time you get to steady cruise state. My TPS seems to respond very smoothly in diagnostic, to slow deliberate increase in throttle position and goes up by individual numbers all the way to 100. The 101 is not important it could even go to 105 the ECU does not respond passed 100 from what I've read today. It seems more important that the low number is 16 and how smoothly it changes the numbers. I don't think its a TPS problem. After dumping my fuel tank in a white bucket today the garbage that came out tells me I have rust particulate in one or two of the injectors. It stands to reason its more noticeable at slow speed and when you pour the throttle to it, it hides problem because enough fuel is getting through the injector screen. Not sure just guessing. I don't think even Berryman B-12 will dissolve rust though.
 
Time to pull the fuel pump and clean the screen. Also, get rid of any rust in the tank. Fuel injectors should go someplace where they can clean and test as well as replace inlet basket filters. No chemical solution to dealing with particulate rust in the fuel system.
 
you can also check the molex plug from the ignition switch. The plastic plug that allows the ignition switch to plug into the wiring harness. Corrosion in there will also cause these symptoms.

Good luck!
 
Have an 04'. I have had 2 problems over the years which caused "sputtering" or rough or barely running conditions.
1) Bike was running fine. Suddenly it was stricken with a bad miss and intermittent stumbles. As I rode it home in the dark, (hoping I would make it), I noticed a light show down inside the fairing. Closer inspection showed the plug wire arcing across to the head. New plug wires. FIXED!
2) Riding down the road. I think in my head "MAN, this bikes just runs so SWEET"! 10 miles later, it is barely running, and I limp home. 4 days from a cross country trip.... A trip thru the forum got me a guy who said, "Check the big white connector, just behind the steering stem, in front/on top of the valve cover." cleaned it up and applied some magic contact cleaner. BINGO! FIXED! (Have since done this to every connector I could find on this 90K bike).
Brad
 
That big white connector is the molex plug I’m describing. If there is corrosion on the big white wire that connects in the plug, the bike will run bad. My FZ1’s white wire was shorted inside the plug. I cut out the white wire from the plug, i soldered the wire back together and the bike ran great.
 
That big white connector is the molex plug I’m describing. If there is corrosion on the big white wire that connects in the plug, the bike will run bad. My FZ1’s white wire was shorted inside the plug. I cut out the white wire from the plug, i soldered the wire back together and the bike ran great.
I may be mistaken but I believe that the "big white connector" (Molex plug) issue is exclusive to Gen I.
Post #42 above suggests that he should investigate fuel pump and injectors for rust particulate contamination.
 
I’m having the same type of issue. 2005 fjr1300. Warms up and then starts to jerk and sputter when hitting 4,000 rpm. I’ve put seafoam in and also sentry fuel additive and have had no change. I’m hearing some gurgling noises in the tank after I stop could it be the fuel filter is clogged? I’ve already cleaned the gas cap and ensured it is venting.
 
I’m having the same type of issue. 2005 fjr1300. Warms up and then starts to jerk and sputter when hitting 4,000 rpm. I’ve put seafoam in and also sentry fuel additive and have had no change. I’m hearing some gurgling noises in the tank after I stop could it be the fuel filter is clogged? I’ve already cleaned the gas cap and ensured it is venting.
Hi Telliott, any updates on your bike?
 
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