98 GTS w/720 Shut Off Mystery

Seadoo is a GTS with the 720 engine, compression is 140 each. Issue is that it starts and runs fine initially but when hot it will shut off when slowing down. Then won't start for unless waiting about 10 minutes roughly. It's done this for last 3 years, and a carb rebuild with genuine parts didn't fix the issue. Happens about once or twice during 2 hours of riding. Any suggestions would be appreciated.
 
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