Jeff,
You have a lot of questions in there.
I'll try to answer the ones I think I can.
1)The "Flying" herald was adopted at the end of 1939. By the late 40's it was almost universal on equipment. It was designed by a woman who worked in one of the Railroad's Denver offices in response to an internal contest to come up with a new, modern logo for the line. The tender heralds were made to lean "forward" on both sides, although there were rare exceptions.
By the way, the "Aspen Gold" and Silver scheme was first seen in the late 40's on several of the D&RGW's Passenger trains, including the "Prospector". Many employees referred to the new paint scheme as the "Prospector". The colors signify Colorado's mining Heratige and are still the official colors of the University of Colorado.
2) Yes, the boxcars in gold livery on todays D&S were selected by the D&S for that use, chosen from the best rolling stock available for service. This was probably done in the 80's or even the 90's.
3) The D&RGW painted the two boxcars in Gold in the 1960's to match the Silverton's consist. They were used primarily for hauling gear and baggage to the "Ah! Wilderness" dude ranch, and for occasional other material that had to be shipped by rail. Remember the "Silverton", train #461, continued to be listed as a "mixed" train until the last day.
Today, the D&S uses boxcars, mostly in red, to carry fire fighting supplies in times of high fire danger, as well as for regular service as needed. For a time years ago, the D&S offered chartered boxcars for camping use at a spot or two along the line, but I don't know if that service is still available or not.
Hope this helps,
Mike