A bit of a rethink.
I removed the front section and positioned the bonnet using some clamps I made up - similar to butt weld clamps. It all aligned pretty well which means the opening for the bonnet is the problem. It seems that when I flared the guards to match the sill I should have ensured the bonnet opening didn't distort, which it has. Arrrr...
I'm going to lay some fibreglass rope along the edge of the bonnet and juxtaposed along the guard while the bonnet is clamped in position and the front section off the car.
If, when I refit, the front section doesn't align with the mounting points on the unibody you will hear me scream wherever you are.