I've been training for this 5K thing for the past 6 or 7 weeks. I did the first week in the Five Fingers; but after the third day, I started getting those little twinges in my calves that signal an impending muscle strain. So, I bought some traditional running shoes: Mizuno Wave Riders and wore them for the next six weeks. But, as the distances increased, I started getting serious pain in my knees, hips and lower back. It would start as soon as I started a run and last the rest of the day - at least. Something was not right.
Am I too old for this? Did I forget how to run? Am I going too far too fast?
Then I remembered: I've run in Mizuno's before. And I stopped using them because of... knee pain.
So, I bought a new pair of Asics Cumulus, a shoe I've used for many years, in the past. Did my three miles in them last night. No pain at all.
Which is not to say Asics are better than Mizunos. But they are clearly better for me. And, if you're trying to run, but finding it hurts too much, try different shoes. It could be that simple.