The wheels "dish" and its true (both lateral and radial) will not have an effect on your chainline. These olny relate to the wheel and it being centered on the hub and with in the seatstays & chainstays. Check the your hub's manufacturer's website for a exploded parts diagram to see if eveything is in its place, I know shimano provides them.
Sheldon has a great article on chainline: http://sheldonbrown.com/chainline/index.html