As the race director for the 7 Sisters Trail Race in Amherst, Massachusetts, which is held on a single track, steep, rocky trail, we used five waves, separated by two minutes between waves. We did not break the race down into five races, just one race. With the ability to sort and print net chip times, you can get results out quickly without having to wait for the end of five races.
That meant a bit of work to set up five corrals, but with only 100 runners going through the start/finish line, and by using two chips (bought from Brian), one on the shoe laces and the other pinned to the bottom of the shorts, we achieved 100% reads.
E-mail me and we can discuss it more, if you'd like.