So here's the final test of the prototype with all SMD lights connected, and transistor drivers for the greens that are in series. Everything cycles properly and the brightness across all colors looks good.
What it's simulating is a "T" intersection, with a main road being controlled in both directions (a traffic light for each direction), and the intersecting road with it's own light, being allowed to go when the main road is stopped and vice-versa.
Now that it's finalized, I need to move on to gluing the SMD's in place, painting the traffic light body, working on how to hang them over the little road, running all the wires through holes to the underside of the layout, mounting the Arduino, powering it, and soldering up the proto board. This project will have taken more time than any other project on the layout so far.