If you go to San Francisco, which I would recommend, get yourself a daily transit pass. You can hop on and off all the city transit, including the cable cars, under one daily fee. Much cheaper than paying per ride.
When I was there, we stayed in the Holiday Inn up town. It was a little run down but clean and tidy and right at the end of the cable car line. It was quite a bit cheaper than staying on the waterfront. And since we were really only in our room to sleep, it was fine. We only had a day and a half there. The first day, we went to Alcatraz and to Coit tower and wandered all over the waterfront. We were a bit shocked when we had to line up at the waterfront to get back on our cable car to the hotel. That did take a bit of time. The second day, we did a city bus tour that was tied into our Alcatraz tour in the morning and then headed out on PCH to get back down to the LA area to meet up with my friends that lived there.
Alcatraz was interesting, depressing but interesting. It was worth going once but I'd never go again. I found it a little creepy.
You definitely need two full days at Disneyland if you want to see everything in Disneyland and in Disney's California Adventure. But look into whether or not you can get a deal on-line somehow for two day passes. Otherwise, it is quite expensive. Make sure you get on 'Soaring California' in DCA - it is a hang gliding simulation over California, complete with smells. It is really cool.
It is really unfortunate that you don't drive. The drive on the Pacific Coast Highway is really kind of cool. We were able to stop for a little bit here and there all the way down from San Fran to Glendale.