That engine uses CDI ignition. Each cylinder has it's own ignition system. All they need are triggers from the stator and battery voltage. They do the rest in getting the plug to fire. CDI has a www site and includes troubleshooting aids. If you have enough trigger to fire a short gap, and since you have 3 separate circuits, I think your problem is elsewhere.
First consideration is that if I read you right all cylinders appear to be experiencing weak spark. That sounds of a bad power source of which all are common. A 2005 is not all that old but the environment in which it has been may expedite corrosive problems.
My last engine was a 2002 model of that engine and I assume yours is pretty much identical......no reason to change just for the sake of change since they had a winner back when it came out in the late 80's.
First, I would follow the black wires in the individual CDI harnesses. I gave my manual away with my boat so I non longer have it so I have to make some suppositions: If you have a black wire in the CDI harnesses, follow those wires all the way back to the battery - large cable lug at the engine. Ensure that each connection to the common "ground" is clean and tight. My CDIs and the regulator rect and maybe the trim relays were mounted on an aluminum plate that was mounted to the engine block but still had a ground wire to the block (where the battery - wire attaches) to ensure a good ground. Check them all out for corrosion. If a screw, back it out and check it and run it in and out several times to make a good connection.
On power, each has a red 12v power lead from the power distribution point which is the input ⅜" stud terminal on the starting solenoid. Check the reds as you checked the blacks.
Next, measure the battery voltage at the starter 12v terminal (to battery -) while you are turning the starter...... while you are cranking the engine. If less than 10v then your problem could be corrosion between the battery wiring (both red and black.....check as described for the CDIs) and the engine or your battery is not fully charged or sulphated up where the internal voltage drop is excessive. Too low a voltage while cranking can surely cause your problem.
That should get you started.....moving toward a satisfactory conclusion, and yes, ultimately "get you (your engine) started".
Mark
