Murphy's law always applies...at least for planning purposes. As promised, some background and thoughts on the potential challenges and emergencies. You'll notice, my focus is on prevention first.
Wind
ALL of the folks who have floated even significant distances, if not the whole length, of the Missouri have mentioned the wind. It's cost them days on the reservoirs where there is little to no current. I'm retrofitting our old fiberglass canoe with a simple mast/sail, will have extra paddles, and am exploring other supplemental propulsion options. Also packing several pairs of gloves and planning on perpetual spaghetti arms.
Weight of gear
A couple of dry barrels will provide about 50 lbs of buoyancy as well as significant real estate for storing gear and keeping it dry. I'm adding stabilizers to the canoe (design TBD) which will help counter the heavy weight of the gear. I've also included bow and stern flotation bags. I anticipate 300-400 lbs at the times of a full load.
Portaging
300-400 lbs sounds fun to drag down a road on foot, doesn't it? Not to me, but it's a reality. There are at least 17 portages that I've scouted via satellite imagery. Most look like less than a mile and traversable, if in rough terrain. So, balancing the weight on a portage cart and finding a comfortable configuration with which to pull it are primary goals. I have the cart and some ideas, but this is one that requires some testing, trial, and error to find the best configuration...more to come.
As far as emergencies, of course, the hope is that proper planning and preparation would prevent poor performance. But I'm far from idealistic, and know the unexpected always happens. Enter Murphy's law.
Capsizing
All of the flotation and buoyancy configurations I've mentioned previously are aimed at preventing this, BUT should we find ourselves under water, Hank and I will both have PFDs. I'm a strong swimmer and one of the goals is to teach Hank to swim in the next month. If our buoyancy devices work, even at a sub-par level, it should be possible to right a floating, water-logged canoe and bail until we're freely floating again. I need to make sure all gear is securely attached at all times to the canoe or be prepared to replace it or do without. I'll be traveling with an emergency fund to either fly home or purchase replacement gear. It's hard to know how this one would play out.
Running out of food
This one is tough. I'm planning to fish and gather edibles as much as I can. Learning a small amount of botany and regional survival info. But I'm really working hard at planning and executing the resupplies (mail drops at various USPS locations) since the other is not dependable. I'll also be traveling with an emergency fund to purchase food.
Wild animal attack/Human attack
This one is extremely unlikely. Hank will be my alarm system, avoidance will be our primary defense, and if it does come to attack, bear spray is effective on all animals and humans. Make no mistake, I'll be carrying second and third lines of defense as well. The only difference for me between animal and human attack is that as a human I expect in some way to be able to communicate and navigate the situation differently.
This is far from a complete list, but some ideas to get started.