I can see that you really work things out first Sean, so one thing here to advise you about that you might not expect. When I plug welded that flange at the door pillar I asumed that with everything else in alignment the shut line had to be perfect.. But there was a small amount of tension in the panel which had the effect of pulling the A-post shut line slightly wider than it had been on the dry run. Obviously the door had to come off for welding.
I don't know how you can avoid this but I ended up welding on a very fiddly extension to the vertical end of the wing .on the driver's side.
Equally, you don't want the gap tolerance as good as a modern car because the hinge geometry brings both it and the door leading edge very close to the wing when opening.
I know what you mean Peter, i have clamped the wings in place using vice grips, self tappers and panel pins, all looks great until you fit the front panel then everything changes. And when you clamp the inner arches to the wings it got even worse. That's one of the reasons i had to do so many alterations to the inner arch panels to get them fitting flush with the outer arch.
That's another reason i have gone for fitting it all in one go.
Unfortunately a lot of it is down to the poor quality panels, but also the design of the car. Hence why modern vehicles have all gone away from the inner and outer arches being joined this way. Not only does it prevent alignment issues, it also helped reduce corrosion as the moisture wont get into the seam.