I've taken the redline from K-town to Union Station -- transferred to Amtrak and got off at Solana Beach where there's a bus stop across from the station. This bus ($1.75) takes you to UC San Diego where I always get off so I don't know where it goes from there... Some friends used to transfer at SD union station from the Amtrak to the coaster that goes all the way down to TJ.

It's actually quite easy given the horrid state of public transportation in S. California.

Continental Fan - there used to be a car rental in UTC right off UCSD campus -- I think connected with the Radisson hotel on La Jolla Village Blvd. This was many years ago so not sure what's available anymore but worth a check.