honda bf90 fuel issue

I have been running my 1998 honda bf 90 since april and have had it out about 35 times, it always seemed to run pretty good but would 1/4 of the time need to have the throttle advance and choked to start while out fishing even after it was warmed up about. Today after having it take about 3 to 5 cranks to start when pulling out of the ramp, while flushing it I decided to pull the spark plug boots . When it was running at idling at 950 #2 #3 dont change at all, but when it is about 1300 there is some stall but not near like the #1 or #4 cylinder. I assuming it is the carbs are fouled but could it be that the sync is out of whack on it? Or could it also need new spark plug wires? I just replaced the plugs from the champion that were in it to ngk but it didnt fix the firing issues.

Sounds like you know whats going on with your unit. I agree. Wires come with coils. To get her really puring do what you have already though of, also add a high dosage of Sea Foam to your fuel tank to de carbon unit and free up coked rings. The final touch after 50 or so gallons of treated fuel has been run and spent, have the valve lash checked. Preventive Maintance is the key to Honda Happiness. Thanks Martin

Thanks Martin for the response, I have been running only ethanol free gas with stabil marine and sea foam. It amazing how the engine can sound so smooth for only running on two cylinders on idle. I can foresee a carb rebuild in my future. I kinda new it was coming as when I got it the previous owner let it sit up for a year. I was hoping that after seafoaming it and enough trips it would clean itself out but still seems to be gunked up a little.