Sagebrush,
The boats you use really depend on the type of trip you want to have.
Certainly possible to do this float in rec/sea kayaks. The downside is that it will be more of a "backpack" style trip due to the limited space you will have for equip/water/food.
Most folks do open canoes or a mix of different types of boats. Canoes offer great load carrying ability, allowing you to take more "stuff" including coolers, firepans, potties, etc. We did a dude's trip a couple years ago and and rented a "T-Cat" from Tex's to haul all our crap. Just remember, you become a slave to loading/unloading all that gear everyday.
I think the lower section is just about perfect for a 4-5 night trip. Depending on how much off-water exploring you plan to do will dictate your timeline.
In my mind, fall is the best time of year for this trip. Temps are cooler.....water level is down and campsites are plentiful. Spring trips with high water wash-out the sandbars and make campsites more limited.
Agree with the others, wind is the biggest hassle. It can make for some long days. Better to cover some mileage in the morning before the winds get humping. Funny, the wind NEVER blows downriver.
Tex's Riverways is the only shuttle outfitter I've used. Darren is easy to deal with and communicates promptly via email.
Do yourself a favor and purchase Michael Kelsey's guidebook this winter. There is so much info/history in his books that most other guidebooks don't cover.
Feel free to hit me up with any more questions. I LOVE this trip and would do it every fall (we are going late Sept next year).
Nate