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Left coil feeds 1 and 4...right coil feeds 2 and 3...as long as you stick to this it doesn't matter which lead goes to which plug. Left coil will have one short lead and one long...short =1...long = 4. Right coil leads will be about even in length...doesn't matter which goes to 2 or 3.
It's a wasted spark system so plugs 1 and 4 fire together...2 and 3 fire together...only 1 cylinder in each pair will be compressed and ready to fire when the spark happens, the other will be empty and coming on to it's inlet stroke...
It if is misfiring on one cylinder. The replace the plug wire first. Make sure plug is good. If two cylinders are misfiring, then you will want to replace the cap, rotor, or coil pack depending on what you have.
Probably a gas delivery problem to the carbs. Check the lines and check for a filter in the line or at the carbs. Something is stopped up and it can't get enough gas to go any rpms.
Its definitely sounds like ignition parts or wiring... What parts did you replace on the ignition? I am not sure on the ninja 1000, but some of the Kawi's use 2 pulse (pickup) coils off the flywheel/magneto, You can do a simple Ohm test on these (if applicable). You can also try swapping the HV coils around to eliminate those. Then of course the ignition module, or CDI ... I am sure you probably checked all your grounds and connections...
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