Fabian's bike, is the one and only mountainbike with front and rear disk brakes and a jackshaft, that I've seen, that approaches the kind of build I'm envisaging as your planned build, which is also the type of bike I'm planning to build. Although his is a little cluttered with lights and electronic whizzbangs for my liking.

but that helps him test stuff out, so we can all learn for free from his expensive.. trial and error. *respect*
Should be no problem building a bike with disk brake compatability, if you're using your shift kit.
On racing tandems (road or mtb) they often use both F&R disks, AND a front rim v-brake. This is because brakes convert kinetic energy to heat (and sound) so dragging rim brakes as for constant speed moderation on long hills will overheat the rims causing tyres to over-inflate, possibly causing blow-outs. The tandem riders drag only the disks, then use the front rim brake when they need to brake hard to stop or to slow down. If the disk heats so much that it loses ability to moderate the speed, then the captain will opt to use the rim brakes perhaps 1/3 of the time and the disk 2/3 of the time thus allowing each to cool before reaching a critical temperature and failing. This technique of using the rim brake for the hard braking also has the effect of protecting the front spokes which are stressed under hard braking on a heavily loaded bike such as a tandem. You need a fork with both v-brake bosses and a disk brake mount to do this, or have some type of converter which will be a bit more difficult to set up. A tandem carries a lot more weight than a motorised bicycle with only one rider; so using disk AND rim brakes up front should be unnessasary unless you're pulling a trailer and a lot of cargo on serious descents.
Personally I would not recommend using a dual-pull lever on any type of bicycle brake.