Increasing speed and stride length will cause pain. The muscle is tight and weak from the injury. At this point, you should be evaluated by a sports medicine professional to make sure that a chronic hamstring strain is indeed the problem. Work on flexibility using alternating muscle contraction and stretch may be helpful. Muscle strengthening is also critically important.
Scar tissue is common with any chronic muscle injury.
Deep tissue massage is often helpful. Work diligently on your rehab and be patient. Q. I have been a runner for 20 years, but after a layoff of a few months due to stress on the job, I find that as soon as I am 2 or 3 minutes into an easy run, I suffer severe heartburn symptoms. A stress test has ruled out cardiac related issues. I am now reduced to walking.