Knee pain is a nightmare. Took me months of time to sort mine out, but the 'magic' cure for me was a set of moldable insoles for my road-shoes. A collapsed arch on my left foot was causing the foot to roll 'inwards', causing my knee to try and straighten it out and causing massive pain to the outside of my kneecap after about 10-12 miles on the road.
The other thing to consider is how your feet 'align' during normal walking. I tend to walk toes-out (a bit like a duck!) and most clip-in road pedals don't allow enough 'float' for my feet to pedal in their natural position. A set of 'Speedplay' pedals with 15 degrees of float sorted that one out.
Good luck!