As far as what I would do for the pain is definitely back off some on things that cause it. Or things that you notice you have pain doing. When I say back off, I don’t mean don’t do them necessarily, simply maybe lower the intensity or cut back some and limit things that have high impact on your knee. Foot strengthening and mobility work for the legs such as smashing and flossing and things to restore normal range of motion, would be probably be a good idea before trying to trying to increase your performance in running or anything. I had a huge problem with my calves being overactive from my heel strike and overpronation and compensation from other muscles not working properly. My doctor did tell me that stress fractures are apparently very easy to occur so if you begin to notice any sharp pain or the area being sensitive to touch. Back off the exercises and goto the doctors .
Sorry for the long answers especially since they are kind of vague in the advice area. Hope it helped some though!