I remember reading the manual for the Federal compressor ,
It stated that all rust blemishes and scratches on the equipment were to be lightly sanded then painted with the supplied touch up kit . In my experience its very difficult to match paint exactly ,but close is good enough and it does halt the progress of rust spots . I generally havn't found surface rust on transformer lams to be any kind of issue apart from cosmetic . , I sometimes use a small rotary wire brush in a drill to tidy up transformers and metal work . Ive made my own touch up paints by mixing small pots of humbrol enamel to get close to the existing colour .
Judging from the pictures your best off going down the 'touch up' route ,as the surface is 99% good , its lasted 60 or more years ,with a little renovation work it'll last another 60 easily .