If you flying in and out of San Francisco, I'd go:
SF > LA (down Highway 1 on the coast, as you say) > San Diego > Yosemite > Lake Tahoe > SF
The drive from SF to LA takes a long time down Highway 1. The quickest route is by taking I-5 but that's a loooong and boring stretch of road. But the speed limit is 70mph compared to 65mph for most of Highway 101, which would be another alternative, but I only recommend it if you plan on taking in Santa Barbara.
Personally, I would probably fly to SF and stay there for a few days. Then, drive south on Highway 101 until you reach Salinas (you'll also pass through San Jose, so you could take in Paramount's Great America theme park, the Winchester Mystery House or the Great Mall of America). Once at Salinas, take Highway 68 to Monterey (approx. 20 minutes). Since you'll be in the area, you might as well stop, right? Then, drive south down Highway 1 until you get to San Luis Obispo, where Highway 1 merges with Highway 101. Continue south into LA. Again, this isn't the quickest way but it allows you to potentially (if you want to) see San Jose, Salinas (but only if you like John Steinbeck, there is a museum there), Monterey, Carmel, Big Sur and San Luis Obispo. Plus, the scenery along Highway 1, particularly between Carmel (Carmel is just south of Monterey) and Big Sur, is spectacular.
Have you also considered seeing Vegas? If you stay in LA for a few days, I would take one of those days to drive to Vegas (approx. 5 hr drive). LA is okay but not all it's cracked up to be. It's worth seeing but I wouldn't spend huge amounts of time here (I live near LA), which is why I'd go to Vegas if you have a day or two free).
San Diego is very nice...check out the zoo.
Yosemite is amazing. You will get there early enough in the year so Glacier Point should still be open (I feel a visit to Yosemite is only half complete without seeing the views Glacier Point has to offer).
Lake Tahoe also has some terrific views and scenery. Here is another option: if you do consider Vegas and like gambling, you might also consider Reno which isn't too far from Lake Tahoe and would be less out of the way. The downside is that you'd have to drive across the Sierra Nevadas which can be very hazardous because of the snow and ice, although in Sept/Oct it might not be so bad.
Budget hotels.... usually, Best Western are decent and most of their hotels are a good standard, even those with a low budget in mind. Marriott is always good but has less locations. Motel 6 is very, very average and I'd pick Best Western over them any day but Motel 6 would be okay in a pinch. Holiday Inn is a good chain. Most hotels/motels in the US have swimming pools and hot tubs.
Hope this helps. I've lived in California for a number of years and, while not acquainted with every route etc., I'm happy to try to answer any questions you have.