Items 1 & 3 are the hinges. Loosening the bolts on the body allows the front of the door to move in/out and up/down in relation to the front fender. The bolts on the door part of the hinges adjust the angle of the door and allow you to raise or lower the back of the door ( by the striker plate ) up or down. They also allow the door to move forward and backward in relation to the body so be carefull. Picture 2 is what I would call the striker plate. It must be loosened while you are making adjustments at the hinges. It controls how far the back of the door moves into the body. Set it after you have set the hinges. Allow the properly aligned door to move the loosened striker plate up/down as needed and then adjust the in/out to suit the body. Sorry it's hard to explain. It's best to have two people when you do this and take your time. Be careful you don't move your door too far forward as it can jamb against the fender when it swings open. After your door is set properly you can adjust your windows.

After all is done your door should close nicely but because of the tension required to seal the glass against the weatherstriping they won't close quite as effortless as a car with 'B' pillars.

Jorg

PS. I used the finger of a latex glove in the socket to cushion the bolt heads at the hinges because I didn't want to chip the paint on the bolt heads.