In my opinion to be totally fit you need to be able to run. Running is a good way to tone your legs and improve your cardiovascular capabilities.
Try the sprint/jog/sprint/walk technique for a few weeks.
On alternate workouts instead of just running the entire distance at a single pace, try this:
Jog for the first few hundred yards to warm up.
Sprint for 50 to 100 yards until you are breathing very, very hard.
Jog (or walk) until your pulse rate is nearly back to your normal jogging rate.
Repeat the above until you have completed your 2 miles. Finish with a slow jog so that your pulse rate comes down gradually.
Do the above on alternate running days. Keep track of your times and see if your 17:40 number comes down and if your discomfort is eliminated. And let us know how you do.