It sounds like you already have your answer. If your body is constantly tired and fatigue, and if you feel aching and a lot of pain in your muscles, bones, and joints - and the pain seems to get worse the more you run - then it sounds like your body is begging you to take a break!
The journey to lose unwanted pounds can feel like a long one, especially when you are staying active and doing everything you think you can and the weight still will not fall off. You might actually be surprised to learn that you are probably running TOO much and not eating enough throughout the day in a consistent pattern. Ask yourself a couple questions. The first is to really consider how much you are running. It should come as no surprise that running burns a lot of calories, and therefore can make you quite hungry. If you are running more than thirty minutes a day, you are probably racking up the mileage! And as a result, your body has kicked into overdrive and is asking you to feed it more. But if you are trying to lose weight, chances are you are trying to ignore some of those hunger cues or you might be trying to avoid certain "bad" foods. However, this can backfire so quickly and leave you feeling so hungry that you end up way overeating, which undoes all of your progress and makes it that much harder to lose weight.
I would suggest giving your body what sounds like a much needed break from exercise. And focus on your diet. Be sure that you are NOT restricting calories and are not overly hungry, but are allowing yourself a balanced diet of plenty of fats, carbs, and protein at EVERY meal. You might find that you feel more full and satiated more quickly once you have stopped over exercising and started eating well balanced meals. This could mean that you do not get too hungry and over reat, and will probably help you lose weight.