Your editing was pretty good here! Nice work!
I personally didn't like this song in combination with Madoka but this is maybe just my kind of taste
For your story...sometimes I thought I got it and then I lost it again somehow. I think there was a little bit too much going on besides your main-story. It would be easier to understand if you took a few things out...I'm a very lazy viewer you know xD
But all in all it is a good work