I had another go at winding the roof down manually last night. I pulled the emergency lever under the rear seat. I then wound the roof down as far as it would go. I could lift the back part of the roof with the window in it, but the boot lid cover would not open. It was still locked. Should this come unlocked when the lever is pulled? Looking at the boot lid cover motor, there are 2 very tight cables running off it (not slack). I'm wondering if the issue is either with the boot lid cover motor or sensor.
Interestingly after I put the roof back up and tried the top down button, only the back left window went down. It goes down an inch at a time. The rest of the windows stay up.