Keep in mind the window does not sit inside the opening, it sits in front of it. The seal is what overlaps the opening.
You might lookup the rope technique for installing windows. You essentiall stuff a rope in the seal lip, line it up to the opening and while holding a firm pressure of the window/seal to the opening pull the rope slowly from the inside which draws the lip of the seal over the opening.
This is on an FJ40, but same principle
http://www.ih8mud.com/tech/glassinstall2.php