The pain is one way our body tells us that we are overdoing it. This kind of pain, which develops gradually with exercise and gets better with rest, is especially common during or after running or jumping. Cross train - try swimming or biking every other day instead of running. This will take stress off the painful areas. Although I can't recommend one specific shoe for everyone, look for a mid-price shoe with good stability, especially for the heel.
Some companies market special shoes for pronation or for stability.
But the best bet is to listen to those cues your body is trying to give you. And be sure that your shoes fit well and are not too worn. See you out there - but do take it easy.