Greetings,
I do not have experience of this model so I can not provide you with a 'silver bullet' to cure the problem. However I have tracked down a possible wiring diagram which I attach and hope might help you.
Let's look to basics first. Instead of vaseline on the terminals try plumbers silicon, more expensive but can provide superior results. Disconnect
all of your connections, thoroughly clean them with brake/clutch/carb aerosol spray, pop some
silicon grease in the holders and reconnect. Check that both battery terminals are making a good electrical connection and are secure. Fully recharge and test the battery.
Since you have an operational fan, i.e. the motor operates, then I would suspect that the temperature sensor would be the next and cheapest item to test. Try to suspend the sensor in a container of water, attach an ohmmeter to the terminal and body making sure that they can not get wet and short! Gently heat the water up and watch the meter reading for changes, alternatively try a new unit.
After that it looks like you might need the assistance of a Yamaha mechanic/electrician to test the 'black boxes' especially number 29 rather than the ECU or ask some one who has specific knowledge and experience of the model. Owen at Manchester Extreme might be able to answer your question, call 01614835559
Perhaps my answer might bump your question up and attract somebody else to come along with more knowledge.
Sorry that's all I can think of at present but let us know what you eventually find.
TTFN
Hugh.
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WR250RX Wiring Diagram.jpg [ 369.78 KiB | Viewed 10132 times ]