The 3 cylinder Yamahas are famous for build up in the water jacket. The plate on the side gets so much build up water cannot get through and cool at high speed. Seen it tons of times. It's not a hard fix. Yamaha and salt do not mix too well internally. The larger models I have seen many times while changing the thermostats that they had enough build up that when you go to clean it a hole would be eaten through block.
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