I like going on September rides. The worst of the heat is usually gone, many fewer tourists in their RV's on the road, you're very unlikely to get snowed on in the passes like you might later in the fall. But it is prime fire season in the western US.
My strategy is cross my fingers and hope for the best, there's nothing else to do. Your danger of being immolated is 0%. What your concerns are is smoke and road closures. I think there is almost always a way around although you may be adding a considerable number of miles to your day. The smoke is unpleasant to ride in but for a limited time I haven't found it that bad. Sensitivities vary of course.
Also keep in mind that geographically, this is a huge area. Even a really big fire is unlikely to be in your immediate path. The smoke can blow for a 100 miles or more but it's only going in the direction of the wind so you can probably vary your route and get away from that if needed.
It has rained (and snowed) a lot in California this fall and that's really good news. The entire state looked prepped to go up in flames last September. Even if it doesn't have another substantial rain again this year it should be better in 2015.
As far as water is concerned, don't count on the stores in towns w/ small populations (<500±) to be open. They appear to be under significant economic distress. Carry enough food & water to make it to the next decent size town no matter what the map or the web may say about what's there and you'll be fine. And if worse comes to worse and you are in some trouble, like you're out of water, you can always get help by asking a passing motorist or stopping at a residence along the way. Nearly everyone I've ever dealt with on the road has been great.
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