So the soul gem actually isn't in the Vision because the soul gem is green. You see everyone thinks that the yellow gem in the Vision is different than the stone in Loki's staff when in reality the stone in the staff is actually the same one we see at the end in the Vision's forehead. In the second avengers it can be seen that the yellow mind gem comes out of the original blue stone in the staff when Ultron tries to mess with it. That's why the staff could control peoples minds. The soul gem and time gem are both unknown and will probably be revealed in the civil war movie.