It is OK to start with the exhaust snout centered. Then, at the speed you normally run the boat, if the boat pulls to the right, you move the exhaust snout at the rear to the right in small steps until the boat tracks straight. Actually, you move the front to the left, because that is where the slot is. Be certain that both bolts are tight to avoid losing the snout.
The exhaust snout is also a trim tab: When you move the back to the right, prop wash and forward motion tend to move the engine left. causing the boat to track straight.
As far as not starting when fully tilted down, I am not sure of the cause. Perhaps someone else has had and corrected the same problem.