What was the condition of the old thermostat, any rubbish in the water, was it partially open all the time, did you test it in hot water to see if it opened and closed?
I know with the car, also fuel injected, that if the thermostat is open all the time, the choke system keeps working and you can smell unburnt fuel all the time.
On the border run your bike was running smooth and there was no hint of the unburnt fuel.
Hope the problem was the thermostat and it is now fixed.
WOMBAT changed his thermostat a few weeks ago and the outside of the cover looked a 100 years old but on the inside, it looked brand new, the thought being the only coolant was used with no added water.