Have you considered renting a car?
Car rental is usually the cheapest way to go. The shuttle companies usually charge you PER PERSON, so it can add up quick unless you are a party of one!
You can usually rent at the San Diego local car rentals and drop either at John Wayne airport or LAX for no additional drop fees. Usually about $30-$40 for the 1-day, 1-way rental. We usually pick up the car in our home town of Escondido, which has lots of choices (Hertz, Avis, Enterprise, etc.) There should be local rental car offices in either Carlsbad, Encinitas or Oceanside. I have gotten very good rates by booking Hertz rentals through the AAA website (you have to have your membership number to log in). We have found the 1-way car rentals much cheaper than airport parking if you are gone more than 8 days.
-- Rene McD