So, first I painted the ties... using (of all things) a Martha Stewart craft paint called Multi-Surface Satin Acrylic Paint. It dries nearly flat, and adheres well (read that as slightly better) to plastic than other acrylics. I'm brush-painting, to avoid fumes in the basement, and this is the best option I've found.
There are some good colors available - I purchased a light tan (used below), a light gray, and a very light gray, almost off-white (which I plan on using to highlight specific ties).
I then painted the rails (hard to see here); I like them dark, so I used the Floquil paint markers, using Floquil Paint Markers. The Rail Tie Brown seemed to work best; the Rail Brown was too light for my tastes.
So that brings us to the ballast options. This is experimentation here - nothing's weathered or anywhere near final.
This first one used some grout coloring in a charcoal color - which is a very fine material.
The second was finely-sifted rock material, colored a little w/ brown sanded grout.
The third was less-sifted rock material, mostly gray.
And the fourth was back to the finely-sifted rock, but without any brown added.