I agree that we appear to have postwar Lionel components here. As for the shell not sitting flat on the aluminum, I looked back at your pictures of the underside and saw some obstructions:
With out the shell in my hands it is hard to tell if a razor blade would scrape it off, or if a cotton swap with some dish soap and water would clean it up. Whatever you do, take care.
If that doesn't do enough here are the options I see:
The "Expensive option": Find another shell and see if the holes align better - realistically, this is find another locomotive. However, if you do have another GP shell (even a different road name), it would be interesting to see how it sits on your frame and compare the holes to your existing shell.
The "most factory correct repair": Obtain a pair of new 2328-47 lamp sockets and 530-40 rivets. Compare the replacement sockets to see if the holes have potential for better hole alignment and install if so.
The "correctable farmers fix": Oval out the lamp socket hole(s). Use a normal machine screw through the shell and through the hole and into a matching nut. This keeps the shell original and allows for the more factory correct repair to be carried out at a future date.
The "I'm impatient fix": You can file away at the shell as suggested above, but with the shell being in the great condition it is, I think you would be better off with one of the other options. This is not reversible or correctable.
