Been there, jiggle and shove, while pressing gently down on the window itself.
Note: The first time I tried to put this thing back together, in desparation, I pressed it together as much as I dared, hooked up the wire, threw the key, and pressed the window button (down). The unit jumped right into place. In hindsight though, I realized that all I had to do was push up on the motor while pressing down on the window pane, to draw the motor into place.
Live and learn.