the coolant bottle has been the topic of many discussions. some ppl belive you should leave it becasue they beleive it will recur and pull fluid back into the rad if low.
I however have never seen this actually happen, i removed mine as well as many others. like Snop said the hose from the rear of the case and the clutch cover are breathers, they do not attach to the bottle at any point. they meet at the "t" and then the hose gose over the top of the motor and thats it.. as far as the bottle gose when you remove it just run the samll hose from the cap of the rad down the frame and tie it off.