Hi and welcome, Wonks here.

I'd drill the pickguard holes later after the finish is on. All the time you're wet sanding, there's a risk of water getting in the holes and the wood swelling and the finish splitting, even if you fill the holes with wax first. But others do the opposite. Neither way is perfect. Manufacturers drill the pickguard holes last, so you'll often get some slight finish splintering around the screw holes. But as you say, they are under the guard so small imperfections can't be seen. And a sharp drill, a small punch and tape over the hole locations cam help keep things together.

Yes, you've got a really nice piece of wood for the body there, so maybe a light amber tint and it should be fine. You'll find that the grain filler doesn't really tint the ash at all, it will only colour the grain lines it fills. So you may want to do a light amber stain wash over the whole body after the filler has been applied, but if you rub the body down with turps, white spirit or meths, that will dampen the wood (without raising the grain like water does) and show you the colour you'll get if you put a clear finish on. If that looks fine, then just apply the clear coats. If it's a bit pale for you, then you might want to do an overall weak amber (or similar) stain.

You'll need to sand the grain filler right back to the wood once applied as you won't want to leave a covering of grain filler all over the body. You'll probably need at least two applications of the filler as you say. Don't try and do too much at once as the filler will shrink back a bit as it dries, but leaving it on for too long before sanding back becomes much harder work. So you want to minimise the excess filler applied each time, but then let it dry for a bit and do some sanding back, but leave enough so that it can contract a bit and still be slightly proud of any grain lines before a final sanding back.

Number of coats of finish really depends on the thickness of each layer. There's always a tendency to want to apply too much, which results in runs. You'll need enough thickness to be able to sand the finish flat before polishing it, and that is all going to depend on how well the grain filler works. The deeper the dips left after grain filling, the more coats you'll need.