650 engine runs for a while then cutsoff

I have a 96 650 (single carb) pulled from a waverunner 3. It runs well in the water for 15 to 20min, then will quit and not start, i have had it sit for 1hr then restart. I do not think it is carb related, new carb kit however the plugs that hold the circular disc i put a hole in one of them while installing. I also put new reeds, and tank vent. It gets spark when it still will not restart. Any thoughts? possibly stator, go thru carb again?
 
Sounds like it might be overheating. Do you have a pisser? And is water flowing out at a good rate?
Might want to check your coolant line(s) connections, and assure water is flowing throughout.
Less likely, it could be a slow exhaust leak, starving the carb of air. But that would typically clear out in less than an hour. Could try restarting with the hood removed, to see if that might be the problem.
 
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