It looks to me like the legs and mounting brackets on this frame - which attach to the headlamp casing are bent out of true. Certainly the triangular brackets look to have been bent this way and that.
My question - should I be thinking to try and straighten, re-align the headlamp/indicator frame? How would I go about this? (novice ahoy) or simply acquire a replacement? (I've noticed one on a 400 four being broken which has the indicators I need also).
Just bend 'em to what will fit the mounting points, those are much less likely to have been moved - if they are you will have bigger problems than a wonky light mount.
Take all the bits off the front of the bike. (I know, you did that already.) Put the wheel straight ahead and try to fit the frame to the mounts - note where it does not fit, and in which direction (if any) it is crooked. Take the frame to a medium size vice, and bend it to suit. You'll have to fiddle around with deciding which part of the frame to grab with the vice, and what to push on, but it's mild steel and you are going to paint it anyway, so you can go through the grab-bend-fit-check cycle quite a few times.
Yes the ears should be flat - do them with a hammer on the flat at the back of the vice.
I just went through this as I had to bend the ears outwards to fit a 750 headlamp shell; had to soften and re-mould the shell to get it to fit under the keylock and in front of the bottom bar, but I now have a bigger headlamp with that cool clear lens from ebay.