Great trip! IMHO:) I would drive 101 down to the Petaluma find a RV park there, unhook and drive your tow vehicle to San Francisco to do all your sight seeing etc etc. Driving your RV through S.F. is not my idea of relaxing or pleasant, congestion, traffic and white knuckle time:(
After S.F. I would take hwy 37 over to Vallejo then hook up with the 680 back to 101. 101 is a beautiful RV road with lots of scenic sights. Areas I like down 101 are Morrow Bay, Pismo Beach , Avilia beach and San Louis Obispo. All these areas have RV parks and scenic sights to see.
As was mentioned by a previous reply, I like hooking up with hwy. 1 at Oxnard or you can take hwy. 126 at Oxnard right over to I-5 and then continue south. When you get to southern Calif. I would try and plan my travel if possible on the week ends or from around 10am to 3pm or after 8pm during the week days to avoid the cluster of traffic going and coming to work. I-5 is your most direct route from Southern cal. to Yosemite. If you choose to go to Yosemite on the way down on your trip the I would take Hwy 46 at Paso Robles to Hwy. 99. Hwy 46 is a great 2 lane road for RVs. I would strongly recommend you make your reservations today for Yosemite and Sequoia. If reservations are a problem then I would find the nearest town with a RV
park and use your tow vechicle. It would be an easier drive with just your tow vechicle. Traffic through Yosemite and Sequoia can be a cluster of traffic.