As far at the bridge goes, the centre line is probably best referencing it from the centre of the pickup and neck route. As for placement of the bridge, I'd probably tape a couple of pieces of string to the headstock and run one from the treble side of the nut to the bridge and the other from the bass side of the nut to the bridge and move the bridge from side to side till you get the strings nice and even along the line of the neck/fret board. As for scale, I'd moive the saddles of the bridge as far forward and as far back as they will go. Use the mid point as the reference then measure from the back of the nut (where it meets the fret board) to the midpoint of the saddle movement and place that mid point at the length of the scale. Some people measure 1/2 the scale length from the 12th fret. Hope this helps