I just did this in February on Vision of the Seas.
The buses left the San Diego airport at approximately 11AM. They went to the San Diego pier where the luggage was off-loaded, x-rayed and re-loaded back on the buses. Meanwhile, we received a box lunch and a bottle of water.
The trip to Ensenada was smooth and without problems or delay. The border crossing was a breeze, with not a single person being asked questions by Customs. The trip is about 90 miles.
We were taken, as I recall, to the Coral Hotel where in-processing was done. At about 2PM buses were used to transport everyone to the ship.
Hope this helps and that you have a great cruise. If you have any other questions, please don't hesitate to ask.