Hi William,
My knees have also started clicking since ive been training for the FLM, and based on my own medical knowledge(im training to be a vet, but that doesnt mean that my suggestion is correct!!!), i think it is very likely to be due to inflammation of the cartilage around the knee joint, which is caused by continuous pounding from running! I suggest to take ibuprofen and maybe use hot/cold repeatedly after runs to help 1) reduce the inflammation and 2) the hot/cold combination will encourage blood flow in the area, and may help to reduce the inflammatory process! I also bought a glucosamine sulphate plus chondroitin supplement which will help to rebuild any damaged cartilage, and basically save your knees in the future, if taken daily!
Hope some of what i said helps, let me know how you get on.
Charlotte x