Ankles and feet deserve their own entry because they take so much abuse. If you're running the race for the first time, at some point in the race, you will wish your feet could be amputated. No amount of training will prepare your lower appendages for the abuse they will suffer.
Take heart though because for some reason, after the first race, there seems to be some sort of body "memory" and your your ankles and feet won't swell up quite so badly. Even in subsequent races though, you'll have to find ways to cope with foot and ankle pain.
There are several theories about why "Classic Ankle" a.ka. Cankle occurs.
One theory is that physical damage occurs to the bones and connective tissue around the ankles and feet. X-rays on my ankles after my first race found multiple micro-fractures and confirmed this theory to be at least partially true.
Another theory is that the swelling is just run-of-the-mill edema from your body being overloaded by toxins and lactic acid that your kidneys and heart can't process after constant, heavy exercise for days on end.
Whatever the reason, your body just isn't used to the abuse and is protesting. Exacerbating the problem is that the best route almost always crosses numerous small creeks. Your ankles and feet are immersed in freezing cold water and then twisted and torqued in different directions as you travel over large rocks and uneven ground. As most Alaskans know, cold flesh is much more susceptible to damage than warm flesh and your akles are no exception.
Smart racers often take ankle gaitors and wear thick socks to protect the ankles from getting too cold. You'll never prevent them from getting wet, but the protection will help them from getting too cold when you wade through knee-deep glacial water several times an hour.
Be sure to take foot swelling into account when considering which shoes to buy for the race. In other words, err on the large side.
There are lots of ways to cope with the ankle issue and none of them are very effective. Early in the race, you can try to avoid getting your ankles cold, later on in the race, you'll try to find cold water to soak your feet in to keep the swelling down.
Standard coping technique is to take non-steroidal anti-inflammatory drugs (NSAID's). Ibuprofin (a.k.a. Vitamin I) works for the most part and you'll know it's time to take another dose after 3 1/2 hours because when you're really in pain that's when it'll wear off. NSAID's also include Cox 2 Inhibitors which are things like Vioxx and Celebrex. You should be aware, however, that there are serious risks with taking NSAID's on the Classic and other long distance races. By balancing the pain relief with long term permanent body damage many racers opt for the quick relief but this may not be a good choice. You risk serious kidney, GI and heart damage by running for hours or days in a dehyrated state while taking NSAID's. http://sportsmedicine.about.com/od/medicationanddrugs/a/NSAID_endurance.htm
NSAID's are heavily marketed by pharmaceutical companies and you know that what is good for their profit line, can't be good for your health. There are a couple other options. You can either go with a corticosteroid or check out some more natural alternatives. I thought about mentioning a couple of herbal anti-inflammatories but you should probably do your own research. I'm not a medical doctor and herbal medicine is not one size fits all. Herbals are often very effective and can be a good option.
Anyway, back to the feet. Smart racers will find side-trails on the soft forest floor instead of following a rocky creek-bed. Take care of your feet early in the race by running smoothly and lowering yourself off small drops. Don't come crashing down on each foot.
In your pre-race training, strengthen your ankles and lower legs by hiking in shoes instead of boots and going for runs over uneven ground. It's takes time but it will pay off.