Why not try returning a flatter route? Doing a flatter run?
The ankle is OK, I have tweaked it like this a few times before - no real external swelling, something inside that gets better with a bit of RICE and then a little re-training. It should be fine by the British.
The knee is the problem. It seems to be moving OK in all directions, so the swelling up is related to the lump on the inside of the back of the knee and the tendon that wraps the quad around the back of the knee to that point. Other than trying to break that down I don't have any leads on how to stop it happening. Fed up.