Hi Fuzz,
I recently purchased the same kit. I haven't started sanding yet but my mock build revealed similar things to yours. My neck pocket is pretty rough too. My humbuckers didn't fit at all so I've had to route out a little more in each corner of the pup cavity. I didn't notice the fretboard issue but will take a closer look when I get back from holidays. My binding looks about the same as yours in some spots but I've almost finished an esb4 kit which had similar issues straight out of the box and the binding comes up real nice with some careful sanding close to the edges.
Looking forward to seeing how your build goes Fuzz. What colour scheme are you going for?
I'm going for a lemon>cherry>black burst on mine.
Cheers,
Damo