As Phrozin says, 400 grit is really too fine for sanding before staining. The wood surface needs to be a bit rougher to absorb the stain evenly. 180 grit is about as fine as I go if I'm staining. Sometimes you just need to try with a few more stain applications to help level things out. Saying that, your stain finish is only very slightly patchy IMO, and I've seen far worse stain jobs. Sometimes the wood itself has areas with cross-grain patterns in it that absorb the stain in a different way (sometimes more, sometimes less) than the surrounding areas and there's not much you can do about that.
You've also got an ash body and a maple neck, and with the same stain, ash and maple will end up very slightly different colours as the wood colours are that bit different.
So if I'm staining, I often lightly stain, and then use a tinted clear lacquer of the same colour to provide most of the finish before putting clear over that. That generally helps even things out, but it still can't counter some odd grain pattern in the wood that reflects light differently to the wood around it, making it look darker or lighter from some angles.
If you were a big manufacturer, you'd probably chose to paint wood like that with a solid colour, and only chose the best wood bodies for clear/translucent finishes. But when you've just got the one kit and you're set on finishing it a certain way, then you just have to make the best job of it you can and accept small imperfections.