I really loved this!
You got me as soon as I saw the name of the song and the anime. To be honest it got me even more curious to see how you would combine the two!
Story wise I loved it, it's awesome! The scenes you picked are perfect and they tell your story pretty well. To be honest, I don't think it was confusing at all. The real story is nothing like this and I love the anime, though even that didn't stood up on your story. I understood what you were trying to tell us.
I have to agree with Emong though, about the sync. I can't remember the name of the instrument played with this song in english, but with a song like this I think it would be best to go on with the lyrics and only some hard beats. Some hard cuts were ok, but others... I personally didn't like them much, because 1) there was nothing on the song to justify that and 2) some scenes lost their impact, like the one where she leaves the room.
Overall, I think you did well! I liked it. I wish people would edit more with this anime
Also, great banner! It's really pretty and emotional