Are you resting at least one day a week? Rest days are important. Without them your body isn't able to build new muscles and repair properly.
Food wise, are you eating enough complex carbs? Complex carbs supply your body with glycogen. Glycogen lives (amid other places) within your muscles. If you don't replenish the glycogen after eat run you will feel fatigue and eventually enough to affect your running.
If your trying to lose weight, are you doing so slowly? too much too fast could result in your body trying to slow down and using up all its glycogen stores in a bid not to lose weight (it gets scared, things your never going to eat again, tries to shut down). You need to lose weight slowly to prevent this from happening. Your body can only metabolise 2lbs of fat per week, any more then this and your losing glycogen and fat, both of which can and will affect your stamina.
