Sometimes, the best way to re-program the subconscious mind is to do physical activities. If you want to get more comfortable with running, then practicing running is useful. Learning to tolerate exercise "pain" is a learned process. It's physical. But it can be mental also.
When I had two molars extracted, I conditioned myself subconsciously with self-hypnosis AND physical methods. It worked well. I have seen "hypnotherapists" who attempt to use self-hypnosis for the dentist. It did not go as they had planned. When the Pain Control Course is released, I will be teaching you how to use saiminjutsu techniques for dental and other pain control.