Hi all who responded to my request for advice.
Update I have now removed both windows from the doors, but with the outed rail still attached, at first it wouldn't easily come out, but after discussions with Andy from NZ I decided to bite the bullet and pull it out, it took some jiggling and with someone else holding the door because I had already removed the door from the car.
It was a very tight fit though, it would be interesting to know what sequence they did the original assembly was. Or if others here have knowledge of the reassembly sequence.
Jack