It seems pretty clear to me that your mind is divided. There is a conflict between a superficial mind and a deep mind. The superficial side is the hunting dog mind that gets excited about ideas it gets from the world of people: "Oh! I should exercise!", "Oh! I should meditate", "Oh! They say this would be good for me!", "Oh! They say this is the right thing to strive for!". While the deep mind is not so gullible and does not want to run around like a hunting dog chasing pigeons. As a result of that, you get this sense of fighting between something you think you "should" do on one hand, and not really feeling like doing it, on the other.
This happens when we lose touch with our deeper mind and identify with the superficial. In fact, our deeper mind is always the closest, but we tend to learn to suppress it. Nevertheless, it makes its presence felt by resisting the efforts of superficial mind. Good news is, the fact that it can resist so well, means that it is strong - despite you not giving it a chance to live and express itself.
What my teacher recommended in this case, is to take a step back and see at what point you have alienated a part of yourself. What usually happens is, we want to get something we really want (a job, a girlfriend, a particular place of living), that happens to be incompatible with the deep part of ourselves. At this point we make a deal with our deep mind and ask it to step aside and shut-up for a while, which it kindly does out of its spirit of all-acceptance that is its main characteristic. Deep mind is a mind of great love. So it agrees to step aside, like a good dog, or a favorite childhood toy, or a magic creature from the fairy-tale which used to be our best friend and now gets completely forgotten. The compromise grows and grows, until our life turns into a city without [dogs|toys|magic], but the feeling of something missing remains, and something forgotten reminds of itself through that resistance and doubts.
What my teacher recommended in this case is to sit down and ask yourself: "what do I want?", "what do I really-really want, that I had put aside and forgotten?" - getting into this mood of asking yourself what you want helps re-unite with the deep mind. There is nothing better than getting it back. It is like getting your life back. From that point on it becomes a matter of cultivating this "being truly yourself" mind until it grows strong again. Cultivating deep mind is cultivating energy of your spontaneous fundamental goodness, your own spontaneous Buddha nature, that always knows what's right.
The truth is, you don't have to meditate. You don't have to run. Running was meant to be a way to refresh your body and stir the energy, not a way to torture yourself. So ask your deep mind, and listen to your body - it will tell you how it wants to refresh its energy. Same with meditation. It was meant to be a way to experience peace, to experience suchness - with no judgement, no pressure to reach some target state, to come back to your deep mind - and instead we are turning it into its opposite, some sort of dukkha-hell.
Makes sense? It's a matter of switching perspective. When you get the right perspective, you start working towards the peace of being fully yourself, instead of endlessly frustrating yourself with superficial conflict. It may be scary at first, to be authentically yourself, and may lead to changes in your life situation - and to temporary trouble - but it is endlessly better than trying to do something you don't really believe in.