Well, I took a month off after the DRR 400km. The knee found a new way to complain. I've slowly been building back up. I've even managed a 100km and a 200km. So, in some sense, I'm back to where I was. I've been using flat pedals during the recovery. Cheap ones. They're great. Perhaps they are these, I'm not exactly sure, but it's close:
This has allowed the foot to take whatever position is needed for me not to notice knees and ankles. It's working. I also have metal pedals; but, the plastic provides better traction with my shoes. As a nice side effect, I don't have to have an extra pair of shoes at work to change into after biking in.
I had been using speedplay frogs, and will probably continue to try to do so. But, will build up slowly on those as well.