[busasandrail]

The line on the thermostat housing according to manual is a bypass line to the radiator. It for some reason does the same thing as the big radiator hose does just in a small size. On the stock hayabusa radiator there is two small ports. One is to hook this line to which goes directly into the radiator (not through a radiator cap) *And the other is for the over flow bottle. Mine and a few others have block this line off right at the thermostat housing.
You dont want to hook it to the radiator cap/neck because it will not allow the over flow to work properly. The little hose coming off the radiator cap/neck should go to a overflow/recovery bottle. And you diffently dont want to put a tee in the line because the line coming off the thermostat housing is under pressure which will blow fluid out of any thing its hook to.
This might be why your overheating because when the motor gets hot the excess pressure/water is being blown out the line hooked to the thermostat housing. Basicly leaking/blowning all of the coolant out.

And for the fan running mine does run all the time. *But this could be more because of where my thermo switch is hooked up at. Its on the line between the head and the water pump.