Well I spoke too soon, 2 hrs of perfect running and we lost spark again.
Pulled the ebox and we have about a spoonful of water in the ebox and everything is damp. Just taking the lid off the ebox and blowing it out with air, the ski starts back up and runs fine. Obviously water is getting in somewhere.
No, the ski isn't ever swamped or even run with more than the usual 1/2" of water in the hull they all seem to have. This is not a old crusty ebox, it is very clean and never had any issues with water before.
I checked the ebox for cracks, checked the fuse cover gasket and all the grommets. The grommets all look great, rubber is nice and soft, wires passing thru them are tight where they go thru the grommet. I also used a syringe to dribble water on the outside of the grommets around the wires to see if any water came thru, but nothing did. The ebox gasket is a new Yamaha one, installed correctly and I even put new screws in the box.
I'm at a loss as where the water is getting in, anyone have any ideas. I really don't want to use any sealer on it, that"s not the right way to fix it.