I run the part in question under a wire wheel to loosen up the rust or remove any paint ...
Personally, I would avoid using a wire wheel as you loose the original finish by doing that. Try cleaning the part in a parts washer using a brass brush, then put the part in the evapo-rust. Afterwards, wipe the part dry to remove any of the by-product from the evapo-rust and you are left with the original finish. Spray with whatever rust protectant you prefer.
Removing rust prior to evapo-rust is not needed as the solution will do that work for you. You might be surprised to find paint marks that you didn't know where there! Also, I use paint stripper to remove any paint that should not be there. Again, that doesn't affect the original finish.
Charles' method with phosphate (I can achieve the same finish with zinc versus manganese) works well too.
Regards,
Pete Morgan