As Preston stated, the ignition firing is a different part of the system. Assuming you don't have any gasket leaks on your heads here are some things to try from simple to more involved.
I talked to a guy in your area not long ago that had a similar sounding problem on his HD7000 (which I think is just an HD6000 with the IMheads). He was sure it was his ignition but it ended up being a bad tank of fuel. You can first try a short fuel line right into a gas can of fresh fuel and see if thats your problem.
The second thing to to try and isolate is the Rev Limiter- if its going out it may cause intermittent misfiring. Usually they either work or not but you can isolate that variable by disconnecting the Green wire on the rev limiter to take it out of the equation. Just be careful with your throttle so it doesn't over rev when you check it (especially out of the water- no more than 1/2 throttle and take it up slowly). A good practice is to put a spade connector on the Green wire on the rev limiter so you can easily disconnect it if the motor is not starting.
Finally- make sure you are getting consistent good spark at each cylinder. Use a spark tester of have a mechanic check it. Each of your coils has a wire connecting to a spade connector on the coil base. The wires have a diode on it at each coile and is where the coil is grounded to kill the motor when the key is turned off, kill switch activated, or oil pressure sensor is tripped. If the harness is bad or a wire is pinched and intermittently grounding, it will be causing a cylinder to misfire. When there is a single carb on the motor, this harness is held out of the way of the fan and such with tie wraps on the intake manifold. I am not sure how they do this with the dual carbs but you can try to isolate the harness by disconnecting the wires to the spade connectors on the coils and see if it runs well. This is pretty involved to take off the cowling to get to the coils with the dual carb setup compared to the single carb. If you run it without the harness connected (and cowling off) be careful of the fan blades and note that you will not be able to turn the motor off with the key or kill switch- you will have to choke each of the carbs or use insulated gloves to pull the plug wires from the spark plugs to turn it off.
Hope this helps.
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