I'd suggest that here lies your problem!

Any leak in the cooling system, however tiny, will cause the system to run at a lower pressure than it was designed to do. Water (coolant) in a fully pressurised system running at 20psi (like the XT), will boil at 112C. If you lose pressure, the boiling point will lower itself towards the 100C mark. The whole cooling system will work less efficiently. Coolant loss through the hole will also cause lower levels and air locks in the system and allow air to be drawn in when the bike cools and the coolant contracts, which together will also have the same negative effect on cooling efficiency.

The other issue is the fan only switches on at 102C on the XT (cuts out when coolant drops to 95C). If your system is at low pressure the coolant will be beginning to boil at 100C, the fan isn't going to cut in till after the problems have started, too late to do it's job properly. With a fully pressurised system 102C is fine because that's 10C below the boiling point and precedes any problems giving a decent comfort zone.

In town all the above issues will be amplified because of the lack of air flow. On the open road at decent speeds the fan is not really needed.

Things to do: Fix the radiator, check for other leaks, test the fan operation in the diagnostic mode.

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