I don't run on the days I commute or when I'm taking only one day off commuting (28 mile round trip). In practice, that means lately I only run on the weekend, usually both Saturday & Sunday (4 mile run). Versus running 4 days a week (my norm when not bike commuting at all), my running is a little slower, but not much. I have not noticed any pain or stress associated with combining running and biking. I sometimes notice a little leg stiffness associated with running again after 5 days off, but nothing significant.
Actually, on the positive side, replacing some of the running with biking has pretty much eliminated the shin splints I was experiencing.