you should have a look at the Liquid Logic XP series -- folks take them down the Grand Canyon. Larger than standard WW kayaks -- hatch in back and room in fron for gear, too.
I won't get into a discussion of skills needed to do the trip you suggest or the sections and various difficulty levels -- others may chime in on that.
There are other "crossover" boats such as Pyranha Fusion; they have deployable skegs which help in the flat water sections. You can google XP10 and grand canyon to see video (i know you are not planning the Canyon, but good to see the boat-type.
URCHIN Portable Anchor
Dock & Launch Systems
Cartop Kayak Carriers
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