Super Jet 1990 yamaha superjet not charging battery

It has a 760 wave runner engine and sadly that's all I know. I can see some wires that have been cut and capped. I tested my battery while running and it puts the same voltage as with it shut off. I am trying to post a pic so you can see my issues, thanks.
 

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Hey thanks for your reply. I have not because I'm not sure what the proper way to remove the cover would be. I see 2 nuts on the far left and right sides, and smaller screws surounding the parimeter of the box. I didn't see the point of trying to open the box because if I was to open it, I don't know What to look for.
 
Not a bad place to just take a peek. I once had a Kawasaki with a bad gasket there and water had gotten in and caused all kinds of corrosion. That's where the magneto is, could be something wrong with the charging coils in there.
 
Location
Stockton
Be careful with the charging voltage. I tested two 701's and a kawi back to back all all three skis only put out between .10 and .2 volts over open battery voltage on a quick on work stand no water hose test.

installed an MSD enhancer in a friends ski and wanted to verify it was charging ok, I thought I'd see 13 volts while running. My open battery voltage was 12.1 and running it was 12.26 so I thought it wasn't charging. I did a simple test of all the other skis and found the same minuscule voltages and none of the other skis have charging issues so it was normal condition.

Now had I had it hooked to the water hose and could run the test over time I might have seen other voltage regulation amounts.
 
Ok I'll keep that in mind. I went out to check, replaced the battery and now it seems to not have spark. There is a black and white wire set that was disconnected when I ran it at the lake, the wires have an in line connecter at the bottom of the hull near the head. I connected them thinking it might help but it did not help and maybe added to my list of problems. I tried to disconnect them but I can't figure out how to unclip the connecter. I don't want to break it so I just left it connected for now
 
Interesting thanks. Well I hooked up a new battery and it started every time. Now the next problem is after I crash and restart it, it kind of Boggs and lags for a few seconds then it picks up again. But the final lap was after I crashed , it bogged after restarting then picked up. On the same lap I was standing going strong when it just shut off. The battery was cranking strong but no start. The lifeguard boat towed me in but within the 4 min boat tow, it finally fired up. I'm getting depressed with my new toy.
 
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