ATF is a general all purpose lubricant that is used when assembling air brake devices. I have used it when I've been doing air brake work under the tutorage of a very knowledge air brake man.
I don't know why you should be getting yuk in the valves unless your pumps are putting it into the air system. Maybe the next time you have the valves off you should blow out the piping on the cars. Also check the air filters on the branch pipes.
As to a commercial place doing repair work, I would suggest going to Pittsburgh Air Brake Co., which is a small shop certified by the AAR. They do quite a bit of air brake work for museums and tourist railways. I have seen its stencil on #6 distributing valves, U-12 universal valves and P and K triple valves everywhere from California to Illinois to Pennsylvania.
Brian Norden
Orange Empire Railway Museum