I had little issues like that, as well. Prior to 2010, I hadn't ever run a full marathon because I couldn't train enough. It hurt too much, basically. I was never injured, but just persistent pain and little issues while running.
So, as you're probably sick to death of hearing about, I switched to flat shoes. Mizuno Wave Universe 3, specifically, which is a racing flat made for 1,000 to I'd say 5,000 meter racing.
Changed everything. Changed my running form, I should say, but "everything" fell in line right behind that. All those issues melted away and have, to this day, never recurred, and now I'm able to run as much as I want, train as hard as I want, and so forth, with no pain. It's amazing really. It's personal success stories like this which have made it such a trend. For good reason, in my case. For me, there's no going back, it's not even a question.