The pickups are at the correct locations. On the Cii RIC moved them about an inch backwards to enable slap/pop, and then when they realized that the truss rods can not be removed for service, returned the pickups back to the original layout, so that the rods can be pulled out and inserted back in through the neck pickup route.
The shadow was created as dark wood tends to brighten in direct sunlight. The area that wasn't exposed remained dark.