[Arran]

Is it safe to remove rust on the transformer? It's perfectly safe to use whatever method you like on the bells/covers. If you mean the iron laminations in the core, a small wire wheel followed by something like phosphoric acid should take care of it, or Naval Jelly if you have some, just to kill the rust, you can also paint them black, some companies painted the iron, some did not. However I would suggest using a wire wheel outside, or in a garage, they throw around a lot of dust, and bristles.
Regards
Arran