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Discussion Starter #1 (Edited)
About 2 weeks ago, I purchased a used 2007 Ninja 650r with 8500 miles. It has a scorpion slip-on exhaust, but no power commander.

My problem: I can't ride below 25 MPH without it bucking/surging/popping. My upper body actually is jolted forwards and back at times due to the bucking. Terrifying during turns. I can physically feel the 'popping' through the bike. I believe they're lean misfires. This problem is worst at low RPMs between 3000-5000. It also seems to be worst in 1st and 2nd gear. However, I can feel a slight surging at all RPMs and all gears. When I accelerate, the bike is smooth (though sometimes there is a pop and a split second delay before acceleration). It's not my throttle control. I've ridden my friend's 650r and it is smooooth.

quick summary:
bike surges and 'pops' at constant throttle
worst in 1st/2nd gear
worst at RPM's less than 5000.
problem goes away when accelerating
Doesn't make a difference whether bike is cold or warmed up
bike fires right up and idles well

Things I've done/checked:
PAIR valve has been plugged (problem was present before and after)
IAP mod - configuration #1 (problem was present before and after)
Chain is around 35mm (25mm at the tightest spot that I found)
Tire pressure is fine.
Idle speed is set to 1350 when warm
Battery terminal connections are tight.

Right now I'm thinking maybe the fueling just needs remapped due to the scorpion slip-on exhaust and that I need a power commander, but I don't want to drop the $300 bucks if it's not going to solve my problem, so I want to check other things first.

Any suggestions for trouble shooting? I've only been riding for about 6 months now, so don't be afraid to insult my intelligence. Feel free to point out easy/obvious things that I should check.

Oh, and I'm 100% sure that the 'popping' is not just afterfires from the scorpion exhaust. Before I plugged the PAIR valve, I got plenty of afterfires when decelerating. This is entirely different.
 

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Discussion Starter #3
Engine Vacuum Sync
I'll give that a shot. I should be able to assemble a DIY manometer sometime this week.

Actually I'm wondering if I may have just found the problem...could an electrical short cause this problem? After pulling off some suspicious black tape from the wiring harness under the seat, I found some scary-looking wiring near the ECU that looks like it was chewed by mice. Get ready to cringe:

IMG_1976.JPG

Does this look like a new wiring harness is in order? Or would soldering/rewrapping them be ok? It looks like only the one wire was chewed completely through (repaired by PO with that mess of pink wire), but there are other spots where the wires are exposed.
 

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Hey,

I pretty much have the same scenario. 2008 with 9,000 miles.

When I got the bike it was fine until about 3 weeks later when the surging/bucking happened. Shortly after that the bike started running horribly (very weak, loud misfires etc). It turns out the left cylinder wasn't firing properly. Cleaning the fuel injectors ended up making the bike run brand new but less than 100 miles later the same cylinder (left) is misfiring.

I'm figuring it out now but I ordered an injector cleaner kit and I will be hooking up the power commander that was in the bike (I have an arrow exhaust straight piped). Seems like others with this problem have an open exhaust with no commander. Right now I'm wondering what would cause the same cylinder injector to get clogged in under 100 miles.

Anyway, I'll post when if I find the fix. I hate that people never finish these threads.
 

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I doubt it. There are tiny rust freckles in the gas tank but thats why we have fuel filters. Plus if the fuel was contaminated the right cylinder would fire weak too.
 

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Turns out the fuel tank is rusted pretty badly. The fuel pump contraption was packed with gunk. That would explain the fuel injectors getting clogged again so quickly. Bought a new fuel strainer. Going to clean the rust with the works, then coat whatever I can in Rust oleom and spray some vertical WD40 and shake it around a bit. Then I will clean the Fuel injectors again and the bike should be good to go.

I ride every day it doesn't rain so the tank won't rust the way it did when the bike was used 900 miles per year. If that isn't the solution I will update.
 
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