I hate to say it but it might look a lot better being all black. Or else do what I did on my ES-3 build, where my first sunburst top ended up looking rather like yours and so I took it all back to bare wood and started again.
Headstock doesn't look to bad in the photo to me, especially once you get some tuners and a logo on.
I'd drill your tuner holes before you apply any clear finish, just in case something goes wrong and the finish cracks round a hole or the drill bit slips etc.