I have not taken the drive from Ensinada to San Diego but... I have read many posts on it on Cruisecritic.com. I have also walked though the boarder many many times when we were visiting Tia Juana Mexico from San Diego. Most have written in their posts that the bus trip takes 3 hours or more depending on if they take an extra bathroom break. Could be a little longer or a little less. You may want to book your flight at least 5-6 hours or more since I've heard that the bus loading at the pier can be very slow. You will also need to go though imigration and customs at the Tia Juana boarder. This means that you need to exit the bus go though customs and imigration and get back on. The Imigration line can be long at times depending on the time or day you are there. Good luck :-) and enjoy your cruise.