My wife had a C-section 3, months ago and says it still burns and hurts from time to time is that normal? How long until. She can start safely running

Exam first. Before resuming activity after surgery, especially if there are still symptoms. A person should see the surgeon for exam and suggestions about how to get fit or to resume an exercise program.
Probably. It can take up to 6 months for complete healing after a cesarean. A burning sensation or other pain is common as the rectus fascia, muscles, and skin are healing. Generally, if the discomfort is gradually decreasing, it is not likely to be a problem. The general rule is to avoid heavy lifting and straining for 4 weeks after the cesarean - the she may do whatever she wants, including running, etc.