I wonder why she has not tried to talk to her father's ghost yet? He may know some things.
That was one of the best scenes in that movie, i forgot all about it. I think her dad is there until she and her brother grow up, or until his wife either passes away or remarries, like in the hospital chapter.I'm five years late in reading this comment thread but, still, I gotta make the obvious "GET OFF MY TRAIN!" subway ghost reference.
I think if Miko let her father know that she can see him, he'd apologize, have no more lingering regrets, and disappear into the next world and she'd rather still have him around.