Nate, I wanted to mention this a few days ago when I first read this thread, but I got sidetracked.
You mentioned that your toes hurt a little after 10 miles or so, from jamming in the front of your shoes? I would say for sure you need to go up a half size in your shoes. When I trained for my first marathon, I thought that my shoes fit perfectly until I started hitting the teens for mileage, at which point I discovered the joy of the black toenail. fit definitely needs to be your first priority, and you need to break the shoes in somewhat before the big event. There are ways to lace your shoes that help keep your heel locked back as well
chafing? definitely Bodyglide, I put in anywhere that I chafe. Be sure to wear the same shirt and shorts/underwear for training that plan on wearing when you do your hike, you often find spots that chafe after long miles that you didn't know about previously.
Food, just a word of advice, if you use gels, you might want to stay away from caffeinated ones, they always send me looking for a bathroom.
River crossing: well, anyone who pooh-poohs your effort because you didn't risk getting decapitated by a boat's prop needs to grow up. That being said, how about bringing a seylor trail boat (much cheaper than an alpacka) and paddling across the river? you could ditch it on the other side (have a friend pick it up later)and as a bonus, you get to look ridiculous, running through the woods with a couple of paddle blades sticking out of your pack.
best of luck!