Hi ldy, I think you should rest up before you cause more damage give your knees time to heal. When you run do you wear a brace of any kind? That would help to relieve some of the pressure the concrete/asphalt puts on it. I am jogging but I do it on a treadmill because it's an easier impact on my knees. I also miss running outside, nothing beats the fresh air and nature but maybe you could run outdoors 2-3x a wk and on the treadmill the other times.
Or maybe you could on alternate days when you're not running, do a brisk walk for the same amount ofdistance. Does speed walking have the same effect on your knees? Also before you go running apply some ointment of your choice bengay,icy hot etc. then wrap with ace bandage and start off slowly and gradually increase your speed. Before you go to bed at night also apply some rubbing alcohol or ointment (I do the alcohol as to not to have my bed smelling of that strong scent).
You might also want to try getting some absorb shock gel insoles, they would help a great deal. As far as your sneakers go they're still fairly new so I don't see a problem there but your workt regimen is quite good, keep up the good work ethic!