After trying the wire brush method and discovering that basswood is much softer than that bit of glue I ended up cutting the glue out with a craft knife and the edge of a rasp. I hope the Timbermate can cover a multitude of sins, it has to plug that hole plus all the deep scratches caused using the brush.
I've also enlarged the pickup holes so the pickups will now fit, and I can see now that they are just not parallel. Most people probably won't notice, but except me. But I will have to revisit it before I start with the Wudtone na see if there is anything I can do to fix the problem without making a worse one for myself by damaging the top.
I've also finished sanding the neck (maybe) and it has come up a treat. My neck has some amazing grain figures. I'm really stoked with it.