Well, I don't think your outboard has the on engine water separator.
But, if you have an add on, it certainly wouldn't hurt to check that.
As I said about the later model, I have no experience with this engine either....just offering some things to consider.
In the case of the '06 carbed model, the alternator is the "heart" of the ignition system.
With misfires and alarm occurring my attention goes immediately to that.
You might want to look at charging voltage to see if that is abnormal. Especially during the misfiring event. Running in a trashcan full of water is probably the best method to try to duplicate the rpm. Although, putting the transmission in gear will probably just push all the water out so getting a load simulation isn't possible. I wouldn't even try that. Running an outboard, in gear, with the prop attached, is dangerous.
I don't know how difficult access is for the electrical connectors for the stator coil (item 3 in link) but removal of the start pulley (item 1) and possibly even the rotor (item 5) may be necessary so you can inspect for anything out of place or loose/missing in there.
Pay particular attention to the pulser coil assembly (item 2) as that is the component that signals the CDI how fast the engine is turning and when to fire the ignition coils.
Check that both sensor hold down bolts (item 10) are present and tight and that there is no sign of either sensor making contact with the stator segment ends.
The air gap between the two sensors and the stator segments is very important and there should be no foreign debris or dirt interrupting the signal. Sorry, I have no specification for what the gap should be. You would need the shop manual for pinpoint testing in that regard.
Check that the pulser plug connector is secure and that no wires are damaged. I suggest unplugging it, inspecting the terminal pins/blades and their sockets for good fit and cleanliness.
Use some spray contact cleaner on those before reconnecting.
Hopefully someone else here with working knowledge of your model can offer some suggestions.
Good luck.