The skirt forming tool worked a treat, but it still took a long time to make the skirt.
First I made a new skirt, drilled the edge with the template, then bent the edge using the skirt tool. I wasn't happy with the edge distance on the upper doubler, so I made a new one of those, then drilled the upper edge with the template and match drilled the lower edge to the skirt using washers to simulate the plexi. I then clamped the plexi in the right place and match drilled the upper doubler to the steel frame. From there it was a simple case of fitting and removing the skirt about 5 times to match its shape to the right glare shield and fuselage side.