what you need to do is adjust the window not the roof.
if you dont have evidence that the roof has been replaced or tampered with then dont touch it.
when i got my cab i had a similar problem but the window was low instead.
take off the door panel and there are screws to adjust the tilt of the window(end where door shut is, torx screw) also there is two bolts high up to adjust the tilt front to back but most important which is not easy to see is a bolt that is the height stop adjustment somewhere in the middle of the door thats what u need, if you have a little play whith all of them you will get there after a few attempts.
what you want is when you go to shut the door the window top edge just touches the rubber seal right below the overhanging flap on the seal just before the door catch touches then when you shut the door it sits nice and tight on the seal and when the door shuts it pushes the window up on the seal.
good luck.