3 quick problems

On aligning the door, you need to align it to the quarter panel, and rocker panel. Then the fenders are aligned from using the door for a reference. The bolts on the door will allow the door to move in, and out. Top, bottom, or both. Keep them just loose enough to move the door. The other bolts that hold the hinge to the A pillar will allow the door to move front to back. Do not use the door latch to hold the door in alignment. It's to keep the door closed, not support the door weight. Also if your door latch pin area on the body is cracked, fix that first. A bodies are known for this.