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I have been having a problem on my '06 F-12x, it keeps blowing the coil fuse causing it not to get any spark, but still turns over, floods, etc. Check your fuses, they are locaed under neath the tool pack area. That whole black peice lifts up and there is a small fuse panel in there just above the jet at the rear.
 

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I do not know of a fuel filter. I know when mine submerged i had water in the tank and it would sputter on the bottom end, i just topped off the tank, and rode it like hell and never had a problem once i ran that tank through. The ignition problem i think is just a short from having taken it apart to get the water out of the cylinders. Its sporadic, and only takes about a minute to fix even when i am stuck in the middle of the water.
 
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