You should easily be able to go to the parks, leave for the ship around 11:30, get to the ship and get checked in around 1:00. Board, have lunch and check out your state room.
Here are some key times:
Although boarding begins at 1:00 PM, they often allow boarding about 12:00 PM.
You should not go to your stateroom until 1:30 PM, as they are not ready until that time.
Welcome aboard buffets are until 2:00 or 2:30 PM.
Safety drill at 4:00 PM.
The Land/Sea package allows you to be picked up at your resort (around 11:30 - 12:30 depending on the resort) OR from the Animal Kingdom at 12:30. When you check in, they will explain how to leave from Animal Kingdom. Again, you may visit any park but you would need to return to the resort to meet your bus (except Animal Kingdom. At Animal Kingdom, they will hold your day bags and you can depart from the park)