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I had/have a similar issue, as Mallo does, on a 97 gp 1200. With this one it seems that the relay stuck and it toasted the starter motor. When I touched the - cable to the battery it would spark. So I chased it down to the relay. How in the heck do I get the starter off of this thing? I have a service manual but it doesn't give much info on removing the starter. Does the exhaust pipe/muffler have to come off? As near as I can tell the starter is underneath there. Thanks!

Check your starter as I had similar on a Kawasaki when the starter solenoid had gotten stuck.

I would take the starter out and give it a good clean and spray it with a good electrical Marine spray.
the problem is that the Starters are normally in a hard to get spot when spraying the Ski after a day out on Salt water.
I like to fill my hull with fresh clean water and a good quality salt remover and then spray with INOX after I drain.
I only fill to a level that it flushes the engine mounts and starter as well as any clamps in the lower section you may not easily see.
I found I was having to many problems with my two old Two strokes and sold them both and got a newer Four stroke and haven't looked back since.
I now use less than half the fuel and even though the servicing isn't the cheapest, as it costs me $300 for a proper Yamaha service.
The saving in fuel makes up for that :)
Lucky the starters are not an expensive item for that Ski, good luck and hope that fixes your problem.
 

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I'll check it out thanks! It's funny, I have a 2004 Suzuki 400 atv here that's doing almost exact same thing. I put a new starter on it and got it to run, but, after idling for a minute or 2 it will die and when I hit the start button it just clicks. I check the starter side of the relay and it's sending 12v to the starter. If I wait a few hours it will start, and repeat. A new relay is on it's way.

YouTube on the 787 580 series .... donot know if the 1200 is built the same ..
Good luck ....
BTW ... The contacts in the relay burn ,,, and then potentially stick... My experience was with a 1979 Porsche 924 ...
 
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