Wasn't going to post this as not much of an update, but might as well show which way I went about it and why. In the end I decided to take the time to remove all the rust from the inside of the rails rather than just use a rust converter. This way I could use the weld through primer coating that wont burn off like any other coating I could think of using. I had already removed all the rust from the under and around the fish plates, so why they are left.
The rust converter I had said not to use a heavy zinc coating over it which is what most weld through coating are. Not sure if the copper based ones would have worked? Just be aware that not all weld through coatings are primers as well. Only the primer ones can be painted over later if needed, so read the instructions. Wont matter in this instance as will be fully boxed.
I wanted a better way of hanging the leads and gun off the mig when not in use. So I cut a used wire spool in half and bolted one each side. No more leads getting caught up in the wheels when pushing it around.