sfxmum,I'm not a physio or a medic but have suffered knee problems myself.
For me, the best advice I had was to strengthen my quads (front of thigh) muscles as they stabilise the knee so the kneecap 'tracks' properly, if it doesn't, that's a definite source of pain as it aggravates the tissues within the knee.
Try standing on the bottom step of your stairs on your bad leg, facing downstairs. Extend your good leg, straight, at an angle of about 15 degrees from vertical, just enough so it'll not catch on the step. Then bend your bad leg so the knee stays in line with the 2nd toe and the good leg drops below the step. Repeat 10 times and do it regularly (3 times a day if poss). As you get stronger, dip deeper then move up to the 2nd step.
If you have a trampoline or mini trampoline, try bouncing on your bad leg, again being careful to keep good alignment.
Make sure you stretch really well after running, (quads, hamstrings, calves) hold stretches for 1+ minutes, and search for ITB (ilio-tibial band) ones online as that can cause knee probs and is hard to stretch.
HTH, and leads to more comfortable running.