in 2 words, beat it... seriously, they take some "massaging" sometimes to get to line up especially when you are trying to fit a new piece to old pieces that are stationary. There will be some compromise here to be sure and you most like will have to accept the lesser of all of the evils you are presented with. I can say that even from the factory they were not all that level or aligned so do what you must to get it as close as you can. That said, look at what is important, generally the trunk fitment is relatively important but you will have a seal there which sits up about an 1 to 1.5". If it is misaligned at the window it will bug you every time you look at it. Don't be afraid to pull up on the trunk gutters either.
