So, this left knee injury is the strangest little problem. I have almost for certain identified what it may be - Hamstring Tendinitis. Left knee, at the back, where the tendons meet the leg below knee, inner side. The pain also creeps up slightly higher..
I managed to find a blog from some bloke that does ultra-marathons, 100mile runs. He managed to win one in fact. He does full marathons in sub 3hrs which is pretty darned good. He mentioned in the blog a week where he had symptoms similar to mine, and he treated it with ice, ice baths etc. He did not drop his mileage at all.
So I have been doing similar. The difference is quite remarkable. I treat it with ice pack, wrapped in a tea towel. I have a rubber/neoprene sock thing designed for a knee, made of similar material to a wet suite. I wrap the ice pack around the knee and slide the sock over it to hold in place. 20 minutes or so, then remove it and leave the sock on knee. I sleep with the support on the knee as well.
I have also been hitting the gym machines really hard. I have been doing leg curls to build up the hamstrings and nearby muscles. Even though it hurts slightly in the area where the injury is when I do these curls, my knee is completely loosened up after, and feels perfectly good. Even the day after it feels much better.
I suspect this problem is something similar to shin splints. In that condition, muscle and tendon build up causes tissue and nerve distress, and inflammation/pain. Simply because of the exercise, and the muscle/tendon build up, everything gets squeezed. Over time the body adapts and somehow repairs the problem, and you end up pain free, and stronger.
So I think perhaps what is happening in my knee/hamstring is similar. Muscle buildup, and repeated strain from running motion causes pain and inflamation. Hopefully things will settle down over time. Meanwhile I just need to keep on top of the inflamation and pain, icing, and resting when I have to, and keep the knee supported when I sleep so it is not aggravated.