After a few goes and adjusting the flanges to get a nice close fit I removed the panel, cleaned up all the joining faces with a flap wheel and painted with this stuff:
It's a weld-through primer. I haven't used this before and I can't comment about its corrosion resistance but it seems to do exactly what it claims: it is very easy to weld through.
I clamped it all up with a number of mole-grips and started on the windscreen pillar corners because I reckon that these would be the most obvious if they don't align. The first thing I discovered was...
...lead! - where the original panel joint had been filled. It really doesn't weld very well but after a bit of heating and wiping and welding...
Then just a matter of plug-welding and grinding the 200 odd holes. It took me quite a while to get the technique and it still isn't that pretty but it all gets hidden by the grinder.
And finally it looks like this