In one of my other all-consuming hobbies, I am scratch-building a 1:29 railroad flat car for my garden railroad. It is a model of a steel car with a wood deck, so I'm using the same styrene base with basswood decking that you are. I've cut all of the decking but haven't applied it yet. In my case the decking on the prototype is originally painted the same "freight car red" as the rest of the car but rapidly gets chewed up as loads are nailed to it, scrape along the surface, etc., so it really needs a weathering job done on it. Thus, my plan is to try to apply stain (or a paint wash) first, then small areas of rubber cement, followed by airbrushing the color on, and finally removing the rubber cement to reveal the "raw" wood underneath. Having said all of that, I'm open to better alternatives.