looks like alighnment wasn't their worry. Id probably cut it off again and start from scratch. you could maybe reuse the roof skin if it isn't butchered too bad, otherwise, AMD sells skins. as always, when your redoing it, always prep the area as best as you can before you weld the skin back on.

btw, roof skins really arn't that bad. Id say a lot easier to do than a 1/4 panel.