I, d go with the scratchplate idea, you can buy scratchplate blanks in all kinds of colours, and there may even be a standard one that will fit easily anyway.
I know that there are some folks who have converted Teles into Esquires, and Epi Les Paul Specials into Juniors, by just covering the empty pickup holes with a scratchplate.
Filling holes with timber is a difficult one to get right, and matching the finish is another science in itself. I think your guitar would look awesome with some colours that scratch plates are made in.
Looking at your guitar, could you not use a smaller rounded plate to just cover the cavities, a bit like the old Music Man basses had? That may save all the shaping of one, round the horns of your guitar.
Good luck with it anyway, and post pics of the results.
Sollophonic