Hello Bob,
Start by taking rough steel wool and brushing the rust off the transformer, then work the wool to give a nice, consistent grain across the steel.
Next, take some acetone, mineral spirits, or whatever thinner you have handy and wipe down just the steel end bell, doing your best not to get any on the actual stack.
Find a surplus piece of cardboard that's reasonably big (bigger than 12" x 12") and cut a rectangular hole in it so that it will slide down around the transformer stack.
Spray the transformer cover with a clear coating of your choice, allowing the clear to dry before removing the cardboard.
-PB