[JAMF]

http://www.youtube.com/watch?v=mZ17FbDYZNk

That's a stationary ship.

This instruction video linked below is better and tells you how to adjust, when the crosshair drifts over or behind the target. So this clip, with taking Colhut's suggestion into account, it should be quite possible to hit a ship.
http://www.youtube.com/watch?v=fhIUGccIQd4

As far as torpedo runs, I have no experience. But I do know that you'll have to aim in front of a moving ship far enough to give the ship time to cross the torpedo's path.

As the torpedo will slow down when it hits the water, you'll have to adjust for it's speed.
-Would the torpedo go the same speed as the ship, you would have to release when the ship is at 45 degrees off your nose, when flying at a 90 degree angle to the path of the ship.
-Ship slower than torpedo that angle needs to be less, say 30-40 degrees, depending on speed of ship.