On the Ninja 250, the overflow actually comes out of the top of the carbs, so I believe they have to be really freaking full for the overflow to spit gas out like it is. However, with my gas tank, I noticed that even in the ON position (rather than PRIME, as those are the only two options), my tank was leaking gas.
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I don't know what you changed but it likely was NOT the real pilot (low speed) jet. You need to put a healthy dose of a good carb cleaner, like Berrymans B12 Chemtool or Gumout into your gas and then run it for a while over several days. Then put the original jets back in and it probably will be all fixed. P.S. Carburetor Carburetor (LH ONLY) Ref. 1 1 6030 92081 1 6044 92064 1 6007 13280 e—92063/A ND (16187) (1 61 87A) 16031 92009 92055 . Title: 2012 NINJA® 250R
Connect a clear tube to the drainplug of each carb and secure them to side above the float chamber. Make sure bike is on level ground and unscrew the drain screws about one turn or until you see the fuel rising up in the tube. The fuel level should be between 11.5~12.5mm below the highest point of the float chamber line.
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ninja 250 carburetor problems