Hi Dekka kit looks great. The gap in the neck heel/pocket looks like the pocket could be a bit crooked as well. I'd sand the glue off the heel and try and sand the neck pocket a little using a sanding block.
Glue and finish should fill the gap so I wouldn't worry too much.
The hole in the bridge pup cavity doesn't look like a problem it will be hidden. As long as there's enough timber to screw the 4 screws in the pup ring.
Good luck with the build and glad it arrived !