I just rode from Irvine to Petco this past weekend, and ride the PCH all the time in Orange County. I assume you know how to get out of S.D., so I'll just start at Pendleton. As others have said, remember your driver's license. Depending upon what's happening that day, they may decide that they have to write down your information, eg, driver's license no., name, etc. That'll take a few minutes at most. Don't get frustrated at the grunts at the gate. They don't set policy. Here's a pictorial report from a guy that rode thru
http://www.roadsites.org/losthwy/us-101_ca.html. Also, be aware that once in a while, they do close the base to civilian traffic. You can check its website to see the status.
Once through Pendleton, you'll ride north. No traffic worries until you get to Cristianitos in San Clemente, when you enter Orange County and get back on the road. You'll be on el camino real, and be riding on a road that has 2 lanes of northbound traffic, and two lanes of southbound traffic, with street parking on both sides. In short, it sucks through this stretch, especially through San Clemente, and the harbor area of Dana Point. Just remember through dana point harbor area that you don't follow the signs for PCH 1, because that will put you on the freeway. As for PCH thru laguna after 8:00 am, the riding really really sucks. Kind of spin as fast you can until you get past north laguna, at which point you'll be going thru crystal cove, which has a nice wide bike lane. When you get to corona del mar, the same crap happens with cars parked and two lanes of northbound traffic. It lets up right around Hoag hospital. From there, no worries until Main Street in Huntington Beach. As far as the detour suggested about Santiago Canyon, unless you want to go VERY long, that route doesn't make a lot of sense. You'll be adding a ton of miles to avoid about 8 miles of beach traffic. Pick your poison, although if you're really concerned, you could head up Crown Valley or Golden Lantern, pick up Moulton Parkway, until the bike trail in Irvine, and come in through the Back Bay at Newport Beach. Again, a lot of miles, and at Moulton near the golf course you lose the bike lane.
Once you're through Huntington Beach, just stay on the PCH. There's construction going on south of Warner at the bolsa chica wetlands. At that point, you can jump on the boardwalk and enjoy the scenery. you'll be doing it with tons of dogs, mt. bikes, runners, surfers and teenage bikini-clad women. Once north of HB, you could take a left at the jack n the box at warner and go through Seal Beach without much traffic. You'll pop back onto the PCH right about where the San Gabriel River starts. Stay on PCH for a bit, and you'll soon be at Bellflower/LB state.