I talked to a ranger the other day in advance of my trip and learned some stuff that might be useful to someone else.
1. They don't allow you to cache food in Goat Haunt (I was planning to drop food off there and pick it up on my way across the northern traverse). I'd guess they might do it if you showed up there and asked them, but the ranger I talked to said no. They would have to allow everyone to do it, blah, blah.
2. If you take the boat to waterton in the middle of your itinerary, it invalidates the rest of your permit. Again, you would have to get caught doing it. They can't officially tell you it is ok, but it didn't sound like they were big on enforcement.