Then my partner got lost when he continued down to SD somewhere around the military base (Camp Pendleton?) and even got hassled by the MPs there. I hope things have cleared up in the last 4 years.
I've ridden from L.A. or Orange County to San Diego maybe about 15 times. I've gone through Camp Pendleton quite a few times, but you're allowed to ride on the freeway through there too, which is what I usually prefer to do now, and get it overwith. When you get to Las Pulgas Rd., instead of turning left and going under the railroad and into the marine base, turn right and go under the freeway, then immediately left onto the freeway onramp. Seven miles later, you'll get off at Harbor Blvd, and the traffic light there is the same intersection you would end up at if you had gone through Pendleton, but you'll go straight at the light instead of turning left, then follow the street's curve up a little to the left and around the gas station and head inland a bit there in Oceanside to continue on PCH.
The freeway section has a wide, paved shoulder. It's never very clean, but the cars leave you loads of room, and I feel quite safe there. There is a rest stop in the middle and you have to get off there, just because they don't want the paths of bikes and auto traffic crossing at the on and off ramps, but you can go through the rest stop area without stopping and come out the other end and get right back on the freeway if you want to. I usually stop and refill my water bottles there though.
The ride through Pendleton is more laid back, but I can see how someone could take a wrong turn here or there on the various roads and end up in trouble with the MP.