You need to get the exhaust Y-piece out to get the bolt out of the top of the shock, but I've managed to do that a couple of times without taking the airbox out (most recently about two hours ago).
The book lies
Oh and personally, I wouldn't bother replacing the locking nut. Especially for the �20.33 your Yamaha dealer will want for it. This is not advice by the way, just saying.