O.K. , on the switch box you will find the green wires that lead to the ignition coils, in between the green wires are the trigger coil wires, colors are violet, white...... can't remember the rest, the switch box should be marked with the color of each wire, remember what order they went in, and take the trigger wires off the box. Using an ohm meter touch one meter lead to engine ground and the other lead to each wire one at a time. Any reading means the coil is shorted. If you see no reading then touch the meter leads to two of the wires if you get no reading, move one of the meter leads to another wire until you get a reading. Then try the other two wires. The trigger coils are nothing but a coil of wire with two ends,one end running one cylinder, if you get a reading from one end to ground then it is shorted, if you get no reading between the two then it is open. The open coil usualy results in no spark to two cylinders. While the shorted on can affect just one. (sorry I don't have the wire colors, and what wires are a pair, no service manual at home) If all trigger coil have continuity the most likely switch box has gone out.
To test for bad keyswitch or harness, unplug the main engine harness from the motor and turn it over using a remote starter switch, hooked to the yellow with a red stripe and battery cable positive at the solenoid while checking for spark (spark plugs removed) if the spark comes back then you most likely have a problem in the boat harness/keyswitch/ kill switch. if not then it is in the motor.