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The fuel system is pretty well sealed..so you can more or less exclude that..

That leaves you with the ignition..and..mechanical..

Pull the plugs and see what they look like..black and soot can mean a miss-fire(rich)..

If a plug does look fouled..follow its wire up to the coil (it will be under a water-tight cover)..does anything look "rusted" or wet?..water in here will short out a coil and make you drop a cyl...
 

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Replacing that plug MAY make it run properly again...

But the cause has not been discovered..

Maybe that plug was a little "off" from the start..if so..swapping it out will fix it..

But..if the problem comes back..then you need to look further into it..
 

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I think i would be looking into doing a little testing on the ignition..

I am not sure i am qualified to tell you exactlly where to look on your particular ski..but..

First thing would be to see if the coil that leads to the affected cyl. is recieving a 12v signal..take volt ohm meter..go from batt neg. side to coil..whats it say?(power on of course)..

If the coil shows a signal(12v)..reomove coil high tension lead(plug wire) from coil and switch ohm meter to "ohms"..whats it say?..write it down and look in tech forum for a factory spec..(i have no idea what yamaha set as a resiestance..or if it even has a reseistor in the wire)

If its a little off of that factory spec its ok(0.1 off tops)..those specs are more of an average then a mandate..

If the wire is ok then you now need to check the ign modules and crank trigger..and I fear that if you have not done that before then it may be above your skill level(sorry..not meaning to judge here)..

Aside from that..you might be looking at a mechanical screw-up..ie. rings, piston, reeds/cage or other..a good bore scope helps with this kind of inspection..it allows you to see inside combustion chamber and inspect reeds without breaking the seal of any of these parts..
 
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