You're going to have so much fun!
I think the main thing to always keep in mind is that everything in DL is SO much closer than WDW. You walk across an esplanade to get from
Disneyland Park to Disney's California Adventure, instead of taking a bus/driving, so park hopping is totally different. The majority of visitors to DL are locals, so that affects crowd flow too...but you'll see a lot more info on that in the stickies.
I think the more days the better, but I think you should be able to see everything in 3 days. Like WDW, it's fairly cheap to add on more days. So unless you have a huge family, I wouldn't personally consider it a waste to get a 4 day pass and really only be in the parks for 3.5 days of it (if you had to leave in the afternoon, for instance).
I'm not all that familiar with the dining plan, but I wouldn't get it. Again, everything is SO close, you can walk to Downtown Disney or walk out of the park and across the street and eat at Denny's or other restaurants. I think it's better to be open to eating whatever and whenever you want. (Not getting it would also leave you more open to splitting meals if that's an option for your party's appetites.)
I agree with others that splitting the stay between DL and San Diego is probably best. If you really just want to spend one day/afternoon in San Diego and then come back to Anaheim, then I could see where you might consider just driving, as it would be a lot of hassle to change rooms. But there are a lot of things to do in San Diego, so I think you could spend two days and one night there (or more) and enjoy it. The weather is generally a little cooler than Anaheim as well.
