If you do try the train, be aware MetroLink goes to Oceanside, no farther south. Amtrak goes all the way to San Diego. You do not need a reservation for Metrolink, you can just board the train and roll your bike on. The regular cars have space for a couple of bikes and then there is the bike car with lots of room for bikes. You DO need an advance reservation for a bike on Amtrak.
If if you do try Metrolink, I recommend their phone app for ticketing. The machines at the stations can be unreliable.