For the thief, go to the store keeper in Port Au Prince, he'll tell you about the thief. That's how i got the thief. Try to be throughout with the conversation.
For the courier ship, you don't have to go to San Jose. It will appear to the North of Trinidad, so wait in ambush at Scarborough Cove or Galera Point under a friendly flag to Spain, check the fast travel option twice per day (in game time) for the ship. Just get there around 3-5 days before deadline.
Ok, I didn't try with the store keeper. Thanks for the help, I guess that will work.
About courier ship, I can't hoist any friendly Spanish flag because at the moment I only have French and Pirate flag... :/
I cruised around Trinidad and tobago, but didn't meet that ship. However, I had a similar quest where a captain on the street invited me on his ship and told me about a pirate who is repairing his ship somewhere near Belize. I accepted his offer and we sailed there to plunder that pirate ship (he was carrying a lot of gold). I didn't have any trouble finding him. Wherever I moored near Belize, that ship was there...