Hi Tony, no worries sounds like wiring won't be an issue. Up to you when you glue the neck, some prefer to finish separately and some prefer to glue it and work on the whole guitar. You should be ok to sand the neck and body before gluing the neck. Be better chance of getting a better finish in the neck transition if you set it before the staining and clear coats.
Please start a build diary and post a photo of the neck fit. If there is a gap of about 1mm or more then you may have to glue a thin veneer to the pocket. Less than half a mm the glue will fill the gaps