How did you keep the flangeways clear? Are they non-clearing for pizza cutter wheels or are lo-pros not necessary?
I let the spackle dry (flush all the way to the rails), then carefully scraped out the flangeways with the corner of a metal ruler. It wasn't quite wide enough, so then I used a scraper that I made out of a piece of scrap styrene -- and kept slowly making it wider until a car (w/ pizza cutters) and a locomotive (I used a Dash 9, to make sure that anything would run through this trackage) would run smoothly.
I did precolor the spackle, but not to the dark gray of the final paint. You can see the blurry gray blob next to the road at the far side - that's the unpainted spackle. I used black tempura paint (leftover from a kid's art project to precolor - I figured it would be better than leaving it black, as it will undoubtedbly get scratched over time (in fact, there's already a scratch between the tracks that I noticed in the image above that I've touched up already)