hey Alan,
yes glue the neck next before the electronics. Clamp the neck and neck pickup in place and measure the distance nut to centre of 12th fret and centre of 12th fret to both E bridge saddles with the saddles wound forward. Please post these distances before you proceed to make sure you will be able to intonate the guitar ok.
Best way to glue the neck in place is install both E strings and glue the neck heel and pocket and then clamp the neck so string to edge of fingerboard distances are about the same. Wipe off any excess glue as soon as possible with a clean rag. Make sure you use titebond glue. Let the glue dry for minimum 24 hours before you put any string tension on the neck