I'm not an expert in Model RR, but as for weathering I have a little experience. If you have another car, which can be sacrificed, paint it with this same paint, as it looks good for a rusty object, but then I would suggest to take a flat top round brush ( like the ones used in wall stencilling ) not too big in dia. though, and try to dry dabbing some medium orange on the tops, especially where you think sun will strike on, and on the otherside, where you think there will be moisture or could be most of the time in shade and can accumulate condensation or water dripping, try dabbing some dark brown.
A metal piece normally tend to rust alot on the tops where they get wet first, but when it dries up rust tend to turn orange, then the "water paths" stain the side from where it normally drips, and then accumulating in corners or edges of frameworks, that's where the dark brown should be.
I donno about you all guys, but I can speak for myself, that I saw alot of rusted metal in 18 yrs of working in a metal factory
As I said above, if you have another car ( or box car ) to sacrifice, try it out as I explained above. You should see a better result.
No offence about your layout, since U did an awesome job.