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The rear cylinder is not firing, bought new coil and replaced still is not working. Any advice as to what to check next, read on line could be ECU, but that is $700 so don't want to replace unless I know that's the problem.
 

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You need to do more electrical diagnosis. Check for +12v at the coils (both of them), just turn the key on and you should have +12v at each coil. The ECU pulses one of the wires by grounding it which then "fires" the coil at the correct time.

That said....if you have +12v and I'm assuming ground is good since it cranks over and actually runs (on one lung), and assuming that it is the correct coil, there are two possibilities. One, throttle body. Two, ECU. Neither is cheap as you already know.

I know...you're thinking, "what do you mean throttle body?" Well it just happens to be that if one of the sensors in the throttle body fails, and you continue operating the machine with it like that, the ECU will default to killing spark to the rear cylinder. Oh how wonderful that was of Kawasaki to design it that way right? Oh but that's not the best part. The best part is that if it's been running a while on one cylinder, like a good length of time, it can take out the ECU as well.

As a dealer tech, the first thing I do is hook up the diagnostic system and read all of the sensor and error codes. Normally if the throttle body has a failure that causes default to one cylinder, it'll show that the throttle sensor or sub throttle has failed numerous times. That is usually the dead giveaway. But as said, replacing it might only fix the throttle body problem but may not solve the ECU's problem, and there really isn't a way to know for sure which is the culprit short of replacing with known good parts. For that reason, you definitely want to test your wiring to eliminate any of that to be problematic before you spend a bunch of money on an ECU or throttle body.
 
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