Pain is part of the running game. When we jump into training, your legs will hurt. You will be sore. Your shins, thighs, calves, and lungs will burn. This is NOT always a sign of injury. Your body has to adapt to the new strain you are putting on it.
That said, there are times when pain is a sign of bigger problems.
Ask yourself the following questions to figure out if you should back off:
How to Prevent Common Running Injuries By Runners' World
Treat and Prevent Running Injury By Runners Connect
Common Running Injuries: Causes, Treatment, and Prevention By WebMD