Does it have a Power Commander on it? If so, eliminate it and try that. Or it could be the crank sensor or coil.
Did you crank over and check spark on both cylinders too eliminate ignition problems put a plug in the dead cylinder and crank over check for good spark be careful to not touch plug while cranking so as not to get shocked..i would do a compression test to make sure there is no major mechanical problems both cylinders should be within about 10 pounds of each other ... if you have low compression it will have to be tore apart to find cause,,bad rings burnt piston head gst.etc.
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See if you have spark across the plug to the cylinder on both cylinders to determine which cylinder in't firing? I'm not sure how you tested spark plugs?
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