Did you find the offending hole/leak that was responsible for the 1/4" of water?
I know how the water made it's way in... I never sealed the wood box holding any of the electronics or motor and there were big gaps in the top of it. My battery also was wide open in the top. I didn't want to seal things until I had everything straightened out because it would of made it more difficult to service. It also was too cold and snowy to paint and seal things outside at the time. For round 2, I will be fixing all of this.
Here's another build update on the alternator. The magnets are being glued in. As more magnets go in, the more difficult it gets. I did the first 4 last week with minimal drama, as they just wanted to repel each other with a few pounds of force. The next 4 I did earlier today and they were a good bit more exciting. They wanted to be sucked into the center, so it took about 20-30 pounds of resistive force on my part to make sure the magnets made their way properly into their slots. Tonight, I just did #9 of 16 and it was even more difficult. It didn't necessarily want to go in or out of the rotor, but it wanted to rotate axially quite strongly due to both neighboring magnets (NN-SS-NN-SS-NN-SS-NN-SS-) arrangement. With two people and a pile of clamps, we were able to get it into the slot.
4"x1/2"x1/2" N52 Neo's. Most of the reviews online when I bought these suggested they weren't coming apart if two of them came together.