+1
Do this first, but don't route for pickups or drill for the bridge yet. Test fit the neck, then stick a straightedge on either side of the fingerboard and mark a light line down the length of the body (i.e. extending the fingerboard profile down the body). Now get your centerline from these two lines, and you will be guaranteed to have the bridge, pickups, and strings line up properly.
The thinking behind this is that if bridge and pickup positions are determined by the ACTUAL neck alignment, it won't matter if that actual neck alignment is a little off from the centerline.