My buddy's boat motor caught fire

Well it's been a bad year for fishing. A few weeks ago my buddy and I decide to go fishing. We put the boat in and I park the truck. When I got back to the ramp, my buddy had to change the battery. He tells me that the ignition had been left on since our last fishing trip and it ran down the battery. No problem though because he always has extra batteries on board. So off we go to our first spot. He shuts off the motor and we both sit and lather up with sun block. As we stand up to start fishing, he asks me if I smell something burning. We both turn to look at the motor and sure enough, there are flames coming out of it. He gets the cover off which seems to make the flames flare up more. I suggest dumping some water on it, but he says that would be a bad idea. Then he asked me for the water bottle that was laying on the floor. :D I'm pretty sure there was a fire extinguisher on board, but the water bottle was closer. So we aren't mechanics, but it was obvious that the fire was coming from the black box in the rear of the motor just under the fly wheel. So my buddy orders that part and replaces it and we think it's fixed. So last Saturday we take it out. It takes awhile to get it started and it is obvious that it isn't running the same. We start to take off but the motor doesn't have any power. It wont go on plain. There is a strong vibration too. So now my buddy is thinking it's the stator. We hope that's all it is because the next thought is, there is some serious damage to the motor. I was wondering if the timing was off somehow but I sure don't know. If anyone has any thought's, let me know. Fish will be turning on for fall and we want to be there.

No mechanic here, but I would check any wires around the area of the fire to make sure the insulation hadn't melted off and is grounding to the motor. If not I would seek out a mechanic before something worse happens. Just my thoughts, Chuck