Actual calorie counting on a daily basis is fraught with inaccuracies IMO. You're clearly just confusing yourself. If you're eating enough to satisfy your hunger, taking in enough to fuel your running, etc, then I wouldn't worry too much about the figures. As for losing fat and not muscle, and not slowing down your metabolic rate, again I think that your hunger being satisfied by a reasonably rounded diet, and exercising regularly, means this isn't anything to worry about.
If you want to improve anything I think 'tweaks' to your current regime is the way to go, e.g. make sure you get the healthy sources of protein, fat, etc that people are suggesting and generally widen the food groups as much as possible. More veg in place of fruit sounds like a good idea, widen your selection of carbs, and I'm a big fan of all beans and pulses as being good sources of protein, carb and fibre all in one.