I agree with GG - rent a car. I'll be flying from LAX several times this spring and summer. I'll rent a car for the 2 hour drive from my house and drop it off at LAX. I can generally get a rate of about $50 going north, and $30 coming south, with no drop charge. I originate the bulk of my travel from SAN or CLD, but it saves me several segments on a segment constrained RTW ticket to originate and end in LAX.
We've looked at every possible combination and permutation of travel from LAX to San Diego. That includes bus, shuttle vans, limos, train, commuter train, and more. The rental car has proven to be the most cost effective and time efficient method of transport.