Two weeks in and more work has happened than much of the time I have spent. Maybe it is the just that the car is looking more like a car again.
Moving forward (for now) (2)
While work was being done on the roof and c-pillar I worked on cleaning up the trunk. In the process I exposed a couple more rust holes that were concealed under some seam sealer, not big and easily fixed.
The trunk lid was fitted again and my gaps are not anywhere as bad as I thought they were going to be.