What kind of sea kayak comes without a backband, seat, and thigh braces? Do you have sealed bulkheads separating the hatch compartments? Is it a rec kayak rather than a sea kayak?
I've done self-supported sea kayaking trips up to a month, but those were on the ocean or large lakes. You might want to e-mail Ken Whiting with your questions, as he has paddled a sea kayak (sea kayak, not rec kayak) in big rivers with whitewater.
"1. What are the key things I should expect that I would not know from my previous experience."
Navigation skills (chart and compass), if you were on the ocean or large lake. But for a river in the mountain west, you might not need those. Though it'd still be useful for hiking, if you end up doing any.
"2. I am looking for the best methods to prevent boat and gear failure and how to respond when they do fail. What have you done when you swim an and covers get riped off your bow and stern hulls while the boat is recirculated in that big whole you just swam out of? What can I learn from you war stories."
Learn how to recover from a Cleopatra's Needle situation. You need a paddling partner to do it. BTW, those covers are called hatch covers, and the compartments they seal are called bow or stern or day hatch compartments, not bow or stern hulls. And also BTW, if your compartments are divided with foam walls, those might not hold up if the cockpit or hatch compartment gets slammed full of water.
"3. Light weight expedition gear systems for all seasons. What are the great things that work well beyond a dry suite, light weight sleeping bag with goretex bivy? What works better than a poop tube? Whats the best way to meet a fire pan requirement without a traditional fire pan that wights 30lbs? Best water filter systems, best water carrying systems? What is the best long term food system? What is the best way to prevent skirt impulsion?"
Pretty standard answers not specific to kayaking down rivers. Consider using Wag Bags if you don't like the tubes. I use a Sweetwater filter but there are other good, compact filters. Filter from water in a soft bucket (fabric or PVC), not directly from the river. You can dehydrate fruit, veggies, and beef (for jerky) ahead of time, to save money and eat better than living off freeze-dried meals. On my longest trip, we advance-shipped boxes of food to General Delivery at the two towns on our route. Had to walk a bit to pick them up, as post offices were not near the water. You might contact sprayskirt companies to ask what their most implosion-resistance skirts are that will fit your kayak (or have them custom-make one).
If you are paddling a true sea kayak (not a rec kayak), practice not only rolling but edging before you go. You can get away with non-edged turns in a short boat, but a sea kayak will need edging (not just paddle sweeps) to turn quickly. Also, a sudden broach could put you in trouble very quickly, because long sea kayaks just aren't as easy or fast to maneuver as short WW kayaks.