The bolt looks like that because it's been bouncing around inside the valve cover with the engine running ?

just pull the head , you've run it like that for too long that there is carbon and who knows what between the 2 cylinders. you probably don't need to pull the other side after seeing the head bolt missing.

Just jack up the rear of the car and that will lower the coolant enough , water finds it's own level , physics is funny that way ...