If you lift/run then just make a protein shake after. Your diet should already include a lot of pulses, nuts etc. to give you that baseline. Been vegetarian/practically vegan for 11 years now.
Don't overtrain would be my first advice - my wife basically pushed through the pain and destroyed the cartilage in her knees about 10 years ago (when she was just 24 years old). That is the worst thing you can do, so don't push yourself for some arbitrary achievement in running. It's about keeping your heart healthy and clearing your mind.
No Pain No Gain is BS, working through the pain will only wreck your body and inhibit you from doing it long term.
Not a doctor but the stuff that works for me to treat runners knee:
1) Lots of stretching, take a while to stretch the calf muscles especially. The physiotherapist I spoke to mentioned knee pains stemming from tightness around the IT band and shin, that pulling exposes the fat pad underneath the knee cap causing pain when running.
2) Knee guards, they help a little bit to reduce the pain, probably 5-10% during the run
3) Check your shoes, make sure they still have life on them and fit your shoe profile
4) Check your gait, your body structure may be causing your knees to pronate, proper shoes or insoles can correct that