Dale,
I can tell you about most all of the paint jobs. The locomotives had a very simple paint job, black. As far as I know all the locomotives had black boiler jackets, cab, and all the other pieces as well. The rods and stuff were polished steel and the smokebox and stacks were either flat black or graphite. Lettering was white and I don't know of any SV engines with whitewalls or trim. Any locomotive will look accurate in straight black, simple but nice. The early clerestory cars were dark green, and the later turtle backs were salmon pink. Boxcars and stockcars were reddish brown, more deep red than brown, and the trucks, grab irons and the rest of the iron parts were black. They like the engines had white lettering. I'm not sure about the flatcars and gondolas, but I think they were either the same as the stock and boxcars, or were just brown. The tankcar was completely silver except for the the middle which was black. It also had black lettering. The cabooses were red with black trim and white lettering, and were the same color red as the stations, which also had black trim. The reefers were yellow with black lettering and trucks. The sawdust cars were natural unpainted wood boxes, pine I believe, placed on top of flatcars and I don't think they were numbered or lettered. The water tanks were also red with white bases and black roofs. I'm not sure about the logging line colors, but I'm sure someone else is. The best book you could get for reference is Rails, Sagebrush, and Pine by Mallorey Hope Ferrel. Or even better, come out to the SV and see the equipment and locations up close. There is a lot left, and you can get paint samples and stuff. Hope this helps.
Thanks Again, Taylor