Yes, the atmosphere in San Angel Inn is wonderful. Actually, way back when on our WDW honeymoon some 16 years ago San Angel Inn was one of the best meals we had. The romantic atmosphere combined with very good food to make for a memorable experience. Unfortunately, the food quality has declined to the point where the atmosphere just doesn't make up for it.
As for CRT, eating in the castle will be a memorable experience for you. It is kind of neat, even though it is a bit expensive for what you get. But you are going for the experience and not the food.....that's the way to look at it.
Given the list you have, I'd suggest dropping Kona. Not that Kona is bad, but it just isn't as nice as most of the other places you have listed.
Are you going to be on the dining plan? You have an awful lot of 2 TS meals on the list if you are, so you might consider dropping one of those (Flying Fish or Jiko).