yamaha 1998 650 jet ski

I have a 1998 Yamaha 650 jet ski and when the motor gets hot it sounds like there’s a clanking noise in the motor kind of like its firing on one cylinder and has no power at all but when you first crank it up it runs great and it will plane with the best of them what could be causing this? also it will crank on land but will not crank while its in the water what could this be?

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