Hey Luke, no worries best you shape the headstock before the staining/clear coats go any further. You will need to sand the top edge that you cut/shape then stain.
I use super fine steel wool (0000 grade) and carefully rub just the binding trying not to rub any stain off the mahogany or the thin edge on the cap. Others have had success scraping the binding with a razor blade that protrudes from a cut slot in scrap piece of wood at the correct binding width.
I'd rub it back before each following stain coat as it makes it easier than a larger build up of stain at the end of stain coats.
Fretboard you can apply Dingowax. I put multiple coats of tung oil on works well. Some use Dr Ducks Wax fretboard oil and other types of oils.
Good to see you are already thinking about your next build haha