I'm planning on doing the same thing for our cruise, hoping to check in on the the ship by 11:30 or so. Coming in from Disney Springs, I would say aim to leave by 9:00 at the latest. It takes about an hour to get to the port area, so if you arrive at port by 10:00, give yourself about 45 minutes - 1 hour to fuel up, return the vehicle and then take the shuttle back to the ship. I've done a shuttle from the car rental to the ship before (in Port Everglades) and it was fine. I would imagine it would be same experience.