Random thoughts and questions ahead...
So if we start with California, moving around there for a bit. San Diego would be evacuated and be the scene for our storyline with Elizabeth and Samuel. Los Angeles would be a battleground for gang wars. Instead of Bloods and Crips it could be Mara Salvatrucchia against a coalition between the Bloods and the Crips (a coalition threatening to break down at any time). That way Mara Salvatrucchia (I don't know if you know of this gang, but it is a gang originally from Central America who have gained a foothold in the US through immigration) could be the link down to Central America and they could get weapons and such from contacts down south. The Bloods and the Crips could have contacts into the military, giving them access to military equipment in bases abandoned or maybe someone just sells them the stuff. Either way both sides would have loads of weapons, and it would truly be a hellish place to live. The military could be keeping the situation under surveillance, letting them kill each other, and when the winner would try to expand they would attack them. Thoughts?
As for San Francisco it could be fun to do a distorted hippie community. Like take all the negatives from the hippie culture, and turn the positives we can into negatives. There would be rampant drug use, weird religious sects believing judgement day is here, slackers who just wants to see the world burn etc. Just take the City of Love and Flowers and turn it into the exact opposite. Thoughts?
National parks like Yosemite could be where survivalists gather. You know, right-wing nuts with loads of weapons and paranoia, killing everything that looks infected on sight. Or maybe some tree-hugging hippies trying to survive as best they can. Thoughts?
And the highways and interstates could be terrorized by gangs, robbing and murdering those who use the roads. Only the military or those with enough guards/manpower would be able to use the roads. Elizabeth and Samuel would have to take back roads etc. on their little quest. Thoughts?
Since the government planned to nuke the cities in California the military would have withdrawn, and California would have been left to whoever stayed behind. The government might want control of California back, or at least make sure nobody gains enough strength to become a threat. The military could attack anybody they viewed as a threat or potential threat (maybe attack the gangs in Los Angeles when one of them got the upper hand?), establish garrisons in strategic locations etc. Those who still are in California would probably be very skeptical to the government and military, and conflict ensue. Thoughts?
There could be smaller towns/communities still surviving, still just hanging on. Paranoia would be rampant, both because of the disease and attacking gangs or the military, and they would most likely not be very friendly towards strangers. Maybe something Elizabeth and Samuel could run into?
Any particular reason you want the brother and sister to be in Texas? I just have a curious mind.
Just a few thoughts popping into my mind.