There are a lot of factors you are considering, and I have no idea which type of boat will be better for you, but some of your preconceptions aren’t quite right, so let’s start there, and let’s start with the premise that a canoe in this context is a solo boat, rather than a two-person boat to make the comparison more reasonable.
It’s true that in general, kayaks tend to be faster than solo canoes, but solo canoes can be fairly fast in their own right, much faster than most people would expect, if it’s the right canoe paddled by a decent paddler. I think what tends to more often be a significant difference between the two craft is how they handle in strong wind. A kayak moves much more easily in strong wind than a solo canoe (and a solo canoe is much, much easier to handle in strong wind than a two-person canoe that’s paddled solo). You’ll surely encounter quite a few very windy days doing that Mississippi River trip.
As to stability, that’s more a matter of perception than reality. I find that most kayakers (these are average people, not experts), on first getting into a solo canoe, almost always remark about how unstable the canoe feels. That feeling of tippyness is something you get over pretty quickly, but I’d still say that the average solo canoe is more prone to tipping over in rough water than the average kayak (again, there is so much variation in boat styles that a generalization like this won’t be true across the board). In addition, for both styles of boat, there’s just so much that the paddler can do to compensate for any tendency to tip over that stability all by itself isn’t such an important thing. Still, for a person with the skills, a kayak can be recovered in open water by rolling or re-entry, and doing the same in a canoe is just about impossible for most people, especially if the water rough enough to likely be the cause of flipping, and this is even more true for a heavily-loaded boat in rough water. Still, plenty of people have paddled the whole Mississippi in canoes.
As far as ease of carry, the canoe wins, hands down. Canoes are generally lighter, and the fact that they can be supported on your shoulders means the mechanics of carrying is much easier as well. In addition, when it comes time to carry, having your gear in just a few large packs is a huge advantage too, and that can only be done with the canoe. In a kayak, you’ll be packing your stuff in multiple, small bags, and you’ll have what looks like a yard sale going on while packing and unpacking your boat, and you will also need to pack and unpack large packs for consolidating your gear on the carry. Or, you might bring a cart with you and use that to move your kayak without unloading it. Then again, even getting your boat onto dry land and to a location where the cart can be used, without unloading it first, might be a challenge.
Then there’s the learning curve just for paddling. If you opt to use a single-blade paddle in the canoe, it will take two or three years of frequent practice just to develop a decent forward stroke and a good ability to deal with wind, etc. With a double-blade paddle, you’ll be in pretty good control of your boat (canoe or kayak) in a very short time.
A lot of people find that spending long hours in either type of boat is a lot more difficult than they expect. This can be more of a problem with kayaks because in that case, you really only have one position to choose from, whereas in a canoe you can vary how you sit, or switch between sitting and kneeling, or kneel with either leg forward or neither leg forward (both feet beneath you). If you have limited flexibility in your hamstrings, sitting low, as in a kayak, might be difficult without working on it for a while. You won’t know until you start paddling your boat of choice how this is going to turn out, and at that point you may need to think about ways to improve your comfort during long days on the water.
I’m partial to canoes, but for a person who’s mainly just working up to paddling the whole Mississippi River, I’d give the edge to the kayak, especially when it comes to how things are likely to go on windy days. Still, working out how much stuff you need to bring along is up to you, and you might end up liking the idea of a canoe more.