In the last couple of years I ended up with seriously sore feet, or rather one chronically sore foot, as a result of long distances on the road when training for 2012's 50k race and then running it. Variety in training is important; wearing a variety of running shoes; running short and long; flat and hilly; fast and slow in different combinations; and most importantly, running on a variety of surfaces.
Here is a good article on the subject. http://running.competitor.com/2013/11/training/the-importance-of-varying-your-running-surfaces_5889. Good, except it recommends the treadmill! No, no, a thousand times no! I use the stair climber at the gym, as I have probably said before, and the rower and the stationary bike and the elliptical trainer would be OK as well, but I balk at the treadmill. And a better alternative to these would be some cycling, which I may have already mentioned is something I have never done so I am not going to start now. Used judiciously, any of these alternatives can help alleviate the effects of "pounding the pavement". But the main recommendation is to train on ... SAND. GRASS. DIRT. TAN BARK. RUBBER-BITUMEN. GRAVEL. BITUMEN. Varying where you run as much as possible. My only bitumen run now is on Saturdays with a rare Customs race Fridays.