Re: This one will get you thinking
My vote is on ignition and I'd bet it is either the powerpack or timer base.
Take an inductive timing light and tape the trigger shut. Hook it to your battery and put the "clip on" around the plug wires, one at a time. Shut the motor down before changing from one wire to the next. Place the light on the deck or a seat, so that the light can be view easily.
Use the light while running the boat in open water, to see which cylinder, if any, is breaking up.
???