Hi Cade, if the neck was sanded past 240 it will need a few more base stain coats to come up somewhere near the same shade as on the body due to maple being a tighter and harder grain compared to basswood.
Suggest adding another stain coat to the neck & headstock now and if it comes out too dark after a week or so curing time you can take a bit off with a very light 1200 grit wet sanding to help even out the colour.
Cheers, Waz