Uh Oh. Those holes are supposed to line up with each other. We spend the next two hours going over the blueprints of various parts, measuring and checking them out, and finding no issues. So then we start pulling the prints from parts we machined a while ago to measure and check. We even started checking the prints for errors, and found none.
Going back to the Frame print, the first machined piece, we suspect a machining error. But we'll have to take the whole locomotive apart to get measure it. Which sounds bad, but actually I have to take it apart to paint it anyhow.