I would venture to guess its not a crank problem either, however a out of phase crank engine will not run at rpm and will be low on power and also have a noticeable vibration. I have never seen one go "boom" from being out of phase but it really doesnt sound like your problem.
I see you mentioned the dealer tell you to "check the wires under the motor", he was talking about the wiring harness under the motor, that is in plain view now that the engines out, if its not rubbed thru it will be sooner then later and will cause you more electrical issues then you could shake a stick at. Look at it real close and see if any one of the wires is rubbed thru the insulation, when they ground out from bouncing around on the trail the sled will do all kinds of goofy things, seen the tailight harness rub thru and case a sled to have problems. The hand warmers are sent the power from the cdi box, the cdi box gets its power from the staotr and triggered by the p/u coil, this is all in this harness i am talking about thats under the recoil when the engines in and by the coolant bottle and airbox. take out the airbox and check this harness out real,real close.
At the very least you can tape and insulate the harness in plastic automotive convolute tubing to keep it from happening in the future.
I see you mentioned the dealer tell you to "check the wires under the motor", he was talking about the wiring harness under the motor, that is in plain view now that the engines out, if its not rubbed thru it will be sooner then later and will cause you more electrical issues then you could shake a stick at. Look at it real close and see if any one of the wires is rubbed thru the insulation, when they ground out from bouncing around on the trail the sled will do all kinds of goofy things, seen the tailight harness rub thru and case a sled to have problems. The hand warmers are sent the power from the cdi box, the cdi box gets its power from the staotr and triggered by the p/u coil, this is all in this harness i am talking about thats under the recoil when the engines in and by the coolant bottle and airbox. take out the airbox and check this harness out real,real close.
At the very least you can tape and insulate the harness in plastic automotive convolute tubing to keep it from happening in the future.