2004 Yamaha 4-stroke 90hp runs rough.

[jdholt41]

Engine was fine until Yamaha service center touched it. Engine has very low hours. When a timing light is connected to each plug wire we get the same behavior --- The plug fires 3-4 times then misses 2-3 times. Seems like the two ignition coils are not receiving a consistent signal. Plugs and wires have been replaced.
Any help would be greatly appreciated.