1. Stay up in Anaheim, if you can swing it. While there's Disneyland, there's also California Adventure, Downtown Disney, and a number of other things you can check out in the Anaheim area. They have SO many hotels around the area that you should be able to find a great hotel for a pretty competitive price.
2. Maybe I've lucked out, but driving from my house, we can leave at 8 am and still get to Disneyland by 10 - it takes almost an hour to get from my house to the 5, which is then a straight shot to Disneyland. It is definitely true that you need to be prepared for fast drivers out here - they are brutal if you're going 70 in "the fast lane".
3. Gaslamp Quarter, while I've never spent much time there, has really improved (from what I've heard). The new ballpark (Petco Park) is down there, so as they were building, they improved the surrounding area, as well. There's a number of people around there most of the time, so safety should not be an issue (just take basic precautions and such).
4. SD Zoo is huge - the bus tour is a great idea - it takes you around the entire zoo, and they now have the hop on/hop off option (I can't remember if it costs a little more to do that, but it alleviates some of the hilly walking) - since the zoo is in the middle of Balboa Park, there's a lot of building up instead of out.
5. I'm not too familiar with the transportation options of the city (I live about 45 minutes away from downtown), but it sounds like you've gotten a lot of advice from those who would be more knowledgable.
6. I'd definitely second Belmont Park (if you're into roller coasters or "boardwalk games/rides"). The beaches are always great, but very busy during the summer
Disneyland is a lot of fun - I actually prefer Disneyland to Walk Disney World (but maybe I'm biased). California Adventure is right across from the entrance to Disneyland - you can buy the park hopper and go between the two parks all day. There's more to do at Disneyland, but I'd classify California Adventure as a more "adult-friendly" type park - minimal "little kids" rides. Always use the Fast Pass option for the rides that have it - although you can only hold one Fast Pass at a time (from my understanding), it allows you to "wait in line" in two places at once.
Have fun!
Threaded Mode