I won't comment on the wheels or cranks because I know nothing about them - I wouldn't do loaded touring on low spoke count wheels but that's just me. I also don't like proprietary stuff, especially when it comes to cranks etc - unless the replaceable stuff like chainrings and bottom bracket bearings are common and easily found. You guys don't weigh anything so I'd opt for the Dragon Fly version to save weight.
As for running a disc as a drag brake controlled by the stoker (or anyone for that matter) is a bad idea IMO. If you want a drag brake - buy a drum. If not - run the disc by itself. Doesn't sound like your going to be doing any loaded touring - so there really isn't any need for both a caliper and disc. I set up my tandem for a v-brake/drum combo for loaded touring and I normally run just a rear disc.
I've never used seatpost racks - because I never saw any advantage to them - and I also run carbon fiber seat posts and you really shouldn't bolt anything to a pure carbon fiber seatpost that is going to hold any weight at all. Woundup CF posts are different because they are carbon wrapped aluminum. I really like the new Bontrager disc compatible rear rack which can be used with the new Trek bags that snap on and off.