As my recovery moves along this is the question I keep trying to find an answer to. All of my lower leg ailments are almost completely pain free after 7 days mostly off my feet. There is still a little pain behind my left knee and on the top front of my right ankle, but all the swelling is gone and based on my progression I suspect all pain will be gone in another 2 or 3 days.
I have three likely theories as to the root cause of my ankle/lower leg problems. The first, and most obvious is of course my shoes. As many will recall I made a decision to change my race shoe just two weeks before the race. I felt great running in these shoes in that two weeks, but since it was so close to such a long race I never did a long run in those shoes. In fact I don't think I went out for more than 10 miles in them in a single run until the first day of the race. It could easily be that these shoes were somehow lacking in support in critical areas that my shoes I had done most of my long training runs in weren't. Thus my upper ankles needed to make up for this lack of support and after several hours of doing so they just couldn't handle the extra stress that they weren't used to.
My second theory for my lower leg demise is that perhaps I didn't do enough training as slow as I would be traveling in the race. I have no doubts that the overall volume of my training was sufficient but I didn't do all that much training with my sled AND at the ridiculously slow shuffle/speed walk that I would need to do during the race to sustain enough energy for 350 miles. It could simply be that this slower shuffle uses my lower legs in a way different enough from standard running that, just as with the shoes, my lower legs were forced to be used in ways that they just hadn't been used enough in training.
In reality it may have likely been some combination of these two things. But I think even more likely is my third theory: There was an actual specific moment when I first noticed the pain in my right ankle (about mile 25), but it wasn't that I took a misstep or anything at that time. I simply was running along and felt a slight bit of pain there, and then it was gone for awhile, and then it came back for awhile, and eventually it would come back each time with a little more severity. And then eventually I couldn't hardly stand on my feet anymore. The thing is though that I was still able to run all the way up to mile 130. I think it's entirely likely that whatever I did to cause that first little feeling of pain around mile 25 would have normally been no big deal at all. Even if I were doing a long (50 mile) training run I would have been able to finish the run pretty comfortably and I would have likely had a little soreness the next day, but nothing that I would have thought much about. And within another day or two all would have been well and I would have forgotten completely about it. Even if this problem had happened at mile 25 of a 100 mile race I don't know that it would have ended up being that big of a deal. At mile 100 of my race last week I was actually feeling great. Had I stopped at that point I would have certainly had some swelling and pain for a few days but I would have taken several days off anyway from having raced 100 miles and by the time I got back at it all pain would have been gone and I would have once again forgotten all about it. In other words I think what went wrong is simply that I was trying to run one of the toughest races in the world and did a little something to tweak my ankle when I still had 325 miles to go. Over the course of the next 100 miles I favored this leg more and more until finally I began to overwork my other leg, thus the pain in my left ankle and knee.
My solution for the next time around is simple then. I will do what I need to do to cover all of these potential causes. I will train more in the shoes I intend to race in. I will train more with my sled and at much slower pace. And I will hope for better luck. I'm sure if I get lucky and avoid injury next time there will still be plenty of unlucky weather and route conditions that will still make getting to McGrath nearly impossible. And it's this impossibility which has me almost entirely certain that I'll be back out there giving it a try again a year from now.