How long have you had the symptoms?
I used to do interval training and run sprints every day. I started to become weaker and have autonomic symptoms that wouldn't allow for the intensity, but just thought it was hormonal or maybe a thyroid issue until the pain set in. Mine probably took years to develop but I was always strong and healthy until about 2 years ago when it hit me hard. It got to the point that I started to notice a huge increase in pain the night and up to two days after a work out. I ignored the pain and pushed myself through grueling work outs that became more and more difficult (even the ones that used to be easy).Then it got to the point that I actually could not do reps or run. Everything just became worse week by week. It upsets me so much that I can't exercise. I try to go for walks and do light stretches and have to be very careful with my body. I feel like I am 80 years old. I'm still hoping for healing though and think if I am patient and listen to my body, this will get better. It is not as bad as it was, so that is a good sign.
I did some reading about muscle recovery from exercise when the mitochondria are sick. Supposedly it takes much longer when people suffer from CFS, nerve disease, and other illnesses for the repair and recovery of a work out than in a healthy person. I know that to be true for myself for sure.