I'm not sure why you're sanding back after each coat. I'd do a very light sand if there's dust on the finish, just enough to knock that off, but I'd only sand back fully flat after each type of coat. E.g. apply several coats of primer and then sand that back flat, then apply several coats of the colour and then sand that back flat.
You really want a full coat of primer all over the body, but you've sanded back so much with the first colour coat on that you've got bare wood showing again. As I said before, you're very likely that a mixture of bare wood and primer will leave the colour coat sinking in over time into the exposed wood areas and not into the primer areas.
If you are leaving it a week between coats, then I can understand the need to sand it to allow the next coat to key in, but you can simply re-coat after the suggested re-coat period. But even then, you don't need to be very aggressive, just enough to scuff the surface up.
There are so many finishes used on guitars by home-builders and most seem to work that I can't say whether your tin of maple stain and varnish (is that a tinted varnish or two separate tins?) is appropriate without knowing more about exactly what it is you've bought. You'll probably want several coats of the stuff on the neck, and if tinted varnish, with each application it will get darker and could end up looking odd?
I think most people would either use one or two coats of a tinted clear to get the colour right, and then use normal clear on top, or else just use a stain and just clear.
If it is a tinted varnish and you put clear varnish on top, make sure it's the same type of varnish e.g. polyurethane and polyurethane, or acrylic and acrylic.
If you are planning to put a headstock decal on, then you only really want clear over that, and you'll need many coats of clear on the headstock face in order to build up enough depth to 'bury' the thickness of the decal and have enough depth to sand back flat without sanding through to the decal.
On a rosewood board neck, it in normal practice to apply varnish/lacquer to the sides of the rosewood board but not the top. And also to the headstock end of the rosewood board up to the nut.
And you've mentioned that 'double edged sword'. I'd spend a bit of time finessing that headstock shape. It really just needs a bit of extra sanding to smooth off a few bumps. It certainly doesn't need to be a perfect copy of an F-style headstock, but I think it could look a little neater, and now is the time to decide to do it.
Last edited by Simon Barden; 30-01-2022 at 04:33 PM.