The side window support or division bar (just behind the vent) should remain in the car when you pull the molding on the 50 & 51 but I'm not sure about the 49. The 49 set up was harder to work with due to that separate division bar. There may be a screw that holds the division bar at the top. If this is the case, it might affect the molding too. Also check on the bottom of the door for access to division bar screws down there. The molding should come right out since you may have to pull the door panel before you can get to the fasteners at the bottom of the division bar unless the screw are on the bottom of the door. In 1950, they changed the design and put the vent assembly in the door. The door make up should be illustrated in the 1949 Mercury Body Parts Catalogue but I'm not sure if I have the 49 book. Most of my stuff is 50 or 51.
I'm not sure about the 49 but the 50 & 51 cars require a special tool to remove the window crank and that should be the hardest part. The back window vents may stay in the car on Sport Sedans but I'm just not sure about the 49 models.