In my case, I also suspect Sora and Yamato aren't a couple in Tri (they could have broken up in these three years after 02).
However, mi point is that Tri's staff wants to keep their relationship in an unknown state. If Tri's staff wanted to make it absolutely clear that Yamato and Sora aren't a couple, they would have just said it. Instead, they prefer to avoid the subject.
Regarding Taichi and Meiko, I don't see Meiko especially interested in Taichi in Sakai. However, I don't know staff's plans, so I can't assure that they do not plan to develop something romantic between these two characters.
Another thing, I am not interested in Sorato or Taiora, but it isn't strange that Taichi shows concern for Sora. They are close friends after all.