As you rightly say, the rad has the pressure cap, the bottle is purely for overflow. Under pressure the water is pushed past the rad cap an into the overflow. As the system cools, it creates vacum and pulls the requisire amount of water back from the overflow bottle. That's why the overflow pipe feeds into the bottom of the overflow tank.
The fan cutting in when you switch off is due to heat soak. Many bike/cars do this; again, no problem, and to be expected on hot-ish day or after a town bimble.
Rob,understand what you`re saying,but the fan shouldn`t cut in `till 100degrees whether the engine is running or and the guage was only showing just over 80 That`s why I think there`s an airlock or am I just paranoid
Once you've turned it off, the water will take heat from the engine and, to a certain extent, carry on circulating due to the heat (do I mean convection) the highest point will clearly be hotest - - oh, this is where the fan temp switch is - - so the fan starts.
To bleed the system do the following.. (from the manual)
With a 'cool' engine, top up the coolant through the radiator pressure cap (not the expansion tank cap). Allow the bike to tick-over and remove the bleed screw (see pic). Re-tighten this screw, and allow the bike to idle for another few minutes whilst propped up on its side-stand. Finally, top-up the expansion tank to the lower level mark.
(Have to say, the fan on my own bike never activates after the engine has been switched off. Mind you, I do live way oop north near the Arctic Circle (feels like it anyhow!)
Sparkin there are a couple of bleed nipples on the inlets/outlets on the cylinder jackets they are 6mm allen bolts if your really sure theres an air block open these when its cool. you have to take the tank off to get at the rear cylinder vent point though. I can e-mail you a pic if you need as ive just put mine back together. ian.
I have never understood why there needs to be any water in the overflow tank. The radiator cap is sprung loaded to 1.1 or 1.2 bar, depending on the age of the bike, and will therefore only allow water to pass in one direction. The overflow tank is what it says, an overflow, and there is no way for the water to get back into the engine. I have always kept the tank empty and no water has ever appeared.
Tha fact that the cap is sprung loaded WILL allow water to flow in both directions, really.
I have had similar systems installed on many cars and bikes. After a good run, when the temp gets up there is a small amount in the tank, as it cools, it sucks is back in - honest.
Feel the small poppet valve in the center of the cap, that's what it's there for.