Ok - I’m pretty sure I’ve found the problem - the door skins were new repro parts and they look great, but the recess on the inside-top of the skin to accept and locate the top of the guide rod is not sufficiently deep to allow it to sit back far enough to allow the window to sit in the centre of the door frame. I have checked this measurement and it's different on both side of the car (which is why the driver's side is better than the passenger side) and compared it to my brother's '70 Mach1 and his are WAY BACK by comparison.
So - Driver's door, back: (note - you cannot even see the head of the bolt)
Passenger door, back: well - there's the bolt, and the whole setup is much more out into the middle of the door frame
Here's the front of the driver's door - no bolt etc
Here's the front of the passenger door - and there's the bolt, same situation as the rear of the door:
The skins I bought new way back in 2005 so maybe they’ve improved the design since then.
More soon but I need to do some thinking about how best to resolve the problem.