It sounds like you may have Runner's Knee, based on your symptoms.
Here's some info from an article on Runner's World:
To prevent Runners Knee in the future, run on softer surfaces, keep mileage increases less than 10 percent per week, and gradually increase hill work in your program. Visit a specialty running shop to make sure you're wearing the proper shoes for your foot type and gait. Also, strengthening your quadriceps will improve patellar tracking, and stretching your hamstrings and calves will prevent overpronation.
At the first sign of pain, cut back your mileage. The sooner you lessen the knee's workload, the faster healing begins. Avoid knee-bending activities, canted surfaces, and downward stairs and slopes until the pain subsides. As you rebuild mileage, use a smaller stride on hills. Consider orthotics if new shoes don't fix the problem. See a doctor if the pain persists, to rule out another condition.
Something that may help is taking Omega 3 for its anti-inflammatory effects. I hope you get well soon!