Making progress! Have learnt / reinforced / etc a number of things along the way.

1) Tried masking tape for the binding. Silly Sean. Just means you don't get a good smooth flow of wood to binding and there's bound to be a bit of inadequately sanded wood. Had to go back over and do all that again.
2) Be ***king careful with those brushes and Goof-off! I'm not sure how well it worked with removing the glue, or if I've just sanded back so far to removed the gouges that the brushes leave in the wood! Its looking better now anyway.
3) Just keep sanding.

Fret positions measured - they're more precise than I'll ever be with the instrument
Have made a small piece of offcut veneer on backing to play with stains and sanding
Pot holes have been enlarged, little bit of sanding around neck inset and HB routing means the air gap problem from before is no longer a thing. Got to experiment with that water / iron / steam trick for fixing small dings. It works

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Goof off + sanding works.

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First time ever using wood filler. Was s**ting myself. Especially since I'd added some colour to it.

Other learning point - that stuff will go everywhere! Glad it was water based because otherwise I would have potentially ruined the cap.