I spent another few hours playing with the passenger door to get it aligned right. Due to a good size dent I feel something was dropped on the car by the previous owner that knocked the door out of alignment. With the torsion bar out it is easy to loosen the door hinge bolts and reposition the door.

At first nothing I did with the hinges loosened and the striker pins out got the door to sit right. The bottom would always extend beyond the car, sticking 5mm or so out from the body, when the top was aligned correctly. Then it hit me that I probably needed the striker pins in to help 'suck' the door in when closed. Bingo.

So with the hinges loose and the striker pins out, position the door to where it looks perfect above the moulding line on the door. Take a pencil (t-panel needs to be off also) and trace around the hinge on the rear of the car. This will allow you to open the door and tighten down the bolts, as when you pick the door up it will shift. Once the back is tight and still looks right, your going to need to tighten down the front. This is more challenging because you can't get a pencil in there unless you pull the windshield trim. So just tighten and loosen, adjusting very small amounts, until it fits right.

Next, put the striker pins back in. Keep adjusting until the door closes without hitting or rubbing them, and it sits flush. Please note that with the torsion bar out, the front half of your door will sit below the windshield trim line and front fender line. Once the force of the torsion bar is applied when it is reinserted, it will pick the front up. This will also require you to readjust the striker pin.