The good news about SF is that there is a chance you won't have to deal with hordes of tourists. Just make sure you KNOW your bike will be safe, like locked in your room. Had French couple come through the bike coop in San Diego. They had their bikes stolen in SF. I wouldn't be surprised if their replacement bikes had gone through the stolen bike market.

I would ride all of the route that you are allowed to ride. If I were coming all the way to do the ride, I would want to say I did the whole ride. I rode from Santa Barbara to San Diego with my 11 year old son on the back of our tandem and my 16 year old son on his own bike. It can be done. Many do it. My experience is that motorists are far more courteous of touring cyclists than your average recreational cyclists. Mind the rules of the road and you should be ok.

Though I've not ridden the shoulder of the freeway through Camp Pendleton, I would do it if I had to. It is legal. I think it is less than 10 miles with a wide shoulder. Won't be pleasant but shouldn't be dangerous. Your biggest risk will be flat tires from radial tire blowouts. Though you would likely get turned down at the gate to Pendelton, I might give it a try anyway as it would not be far out of the way. Anyway, last time I rode through Pendleton it was no picnic. Certainly not a highlight. You are sort of dealing with a high concentration of 20 something males enamored with the power and sound of their vehicles.