Realistically, you probably are overtraining. I have worked with a number of personal trainers, every one of them yelled at me for keeping up a schedule like yours, plus I was adding in even more training.

Rest days are important, even recovery days where you go easy. I'm glad to see that most of your cycling is in 2 and 3, I think it's harder to push yourself into the high zones in cycling unless you do excruciatingly tough hill climbs or really max out your speed. I rarelly get over my low zone 3 heartrate when I ride. Running in 4 and 5 is pretty normal unless you are an elite runner, so that seems fine. 6 miles three times a week isn't too much for the average runner, unless it's causing you problems with joints. I just found out I have osteoarthritis eating away at my cartilidge in my left knee - Ortho said joint supplements can help a lot for osteo-based cartiledge loss, but not much for rheumatoid. So take a joint supplement to help maintain what you have.

Have you ever seen a pulmonologist about your breathing issues? You might be able to get some benefit out of one of the inhaled drugs like Symbicort or Spiriva. Worth checking out.

Also, you are very cardio top-heavy in your routine. You need to mix it up, get some strength training in there, and also be sure to work on flexibility and agility, stretching, yoga, that kind of thing. Those can still be a lot of exertion and even burn significant calories, but are overall easier on the body, a slower, gentler kind of workout.

What about your weight? Is it appropriate for your frame size? Is your body fat percentage out of line? You might see what you can adjust in your diet to lose fat without sacrificing muscle. High P helps that. Good fats help that too.

Best of luck.