Remove bypass covers and look at pistons and rings.----Nozzle gasket is a donut around that tube sticking out of carburetor body.---Remove bowl to find it.
Does spark jump a gap of 5/16" on both leads , yes or no ?----Post the actual compression test values you have.----Nozzle gasket is in place ?----Checked reed valves ?
Tested the overheat horn ??-----Installed a new impeller when you got the boat ??-----Inspected / cleaned the carburetors ?----If unit sat for years the carburetors could be gummed up.
Note ----The battery is not used to make voltage to fire the sparkplugs.----All done by the spinning flywheel and electronic bits.----There are numerous wires and connections that could be faulty.----Causing the intermittent spark.
Sounds like it is running on 2 of 3 cylinders.----Test the spark.------Tested your overheat warning horn ?----Test and post the compression values you have now after this " loss of power " incident .
Wrong----It should charge the battery at about 14 / 15 volts just like any other motor.----What reading in ohms do you get on the 2 yellow wires from stator ???
See post #18 ?-----Your answer is ?----I have a 25 Yamaha that I got for a favor for a dealer.----Good looking motor with lower unit missing.----Have not done any work to it yet.
Some simple testing will find the issue.-----But I know from many threads here that folks want to hear about an instant fix.----Reluctant to do the testing.
They are electronic goodies.----So yes there can be poor connections / broken wires.----Do you know what a powerpack does ???-----So switch powerpacks and do your testing.-----Nobody can do that for you from 999 miles away !