So I offerd it all up, and with a lot of pushing, pulling and swearing, I managed to get all the fixings in, but, the mudguard was kinked, and under a lot of stress.... So, scratch head, and back to workbench.
As the inner guard was genuine Yamaha, I figured that would be the best alignment of the mounting holes. But, against my frame, the rear hole needed a little elongation to fit. You can just see it below.
I then had to elongate the three holes in the plastic guard to match the 3 mounts on the inner guard. Once this was done, it all mounted up OK. I had to add a washer to the rearmost mount, on the visible top of the plastic guard to hide the elongated hole, but it's not noticeable.
Below are some general shots of where the build is at.