I have 2 questions for you, are you able to influence the speed of the ship? if you ask, will they slow down to around 10 knots?
The reason is because most of those container ships cruise at 25 knots (almost 29 mph) and the phantom does 27 mph tops in dead calm air (I've clocked mine and this was without a gopro camera and with the original props not the vision props). The second you launch the phantom, you will have to give it full throttle in the direction of the ships travel just to keep up with the ship and even then, you won't be able to keep up. If you can get them to drop down to somewhere near 10 knots, you'll be able to actually get a full pass around the ship.
In an ideal world, if you could get a tail wind equal to that of the ships speed, you could essentially hover above the ship with no input from you on the TX. I'm not saying its not possible to do it, I've seen videos of it being done, just lots of things can go wrong. Even if you got the compass issue fixed up, you still have the flight. Maybe find a big open field and fly it at top speed the whole time. Figure out exactly how long your battery lasts so you can make sure you are over the ship when the phantom starts coming down.