So many helpful pointers and comments above, thank you very much gentlemen.
@KevinR I hadn't spotted that the top of the windscreen is an early MkIII fitting, will this cause issues later down the line? I'm happy to replace if sensible (it's not in great nick anyway).
As suggested I've focused on aligning the bolts at the back (I've not got my hands on the correct spacers and fitting yet), the below images are the result, suggesting the windscreen rake is rather out.
I've also tried the windows (didn't think of that, I've always got the wound down!) and there are issues there too. It's a bit tricky to see but there is a lot of overlap when the windows are fully wound up and the door won't close (1st and 2nd image below). This also points to the windscreen rake being off I think?
When I wind the windows up, as high as they'll go with the door closed, there's a significant shortfall (3rd image). I can adjust the window mechanism a bit but I'm guessing start with the windscreen alignment then do the windows if needs be?