Given all the upgrades you're considering, my recommendation would be to consider a complete tandem upgrade to the second generation T2000. Seriously, with various upgrades that you're mulling over -- $550 for a Bontrager wheelset, $550 for a carbon fork, and brake changes yet to be defined for another $100 - $200 -- and the residual value of your current Trek tandem, you're within a few hundred dollars of a NOS '06 Trek T2000 that comes standard with all the parts you're after (but you'd still want to add a compression spring to the Avid). Moreover, when Trek redesigned the T1000 / T2000 framesets back in '06 they fitted a proper I.S. disc mount and curved rear stays to accomodate a 203mm rear disc along with a drilled rear brake bridge for a rear caliper. Just something to consider. I found myself at a similar crossroad only about 7 months when I realized that no matter how many components I changed on our first tandem, it was the limitations of the frame that I was struggling with. I fixed those things with a new tandem frame that -- 10 years later -- is still a joy to ride.
OK, now that I've got that off my chest...
1. As much as I don't like them, to really beef up your rear brake power you might consider going to a Shimano LX V-brake with a Problem-Solver 'Travel Agent' or Sidetrak 'Brake Pull Booster (BPB)': probably about $50 all told. The LX is suggested as a way to minimize the potential for brake squeal that sometimes comes from the brake pad alignment linkage on the XT models and, well, they're very strong and very inexpensive. That would give you the most amount of rear brake power that you can get with a rim brake.
2. You can probably "fix" your stoker controlled drag brake to work "better" with the compression spring that MrFish mentioned and provided a link to and by making sure that the spring tension screw is set to it's highest tension. I'd also investigate your cable routing to make sure that it's as smooth as it can be. Running full-length cable housing isn't awful, in and of itself, but the glue-on / zip-tie on cable guides are a better choice.
3. The "ultimate" hybrid system is probably counter-intuitive, whereby you'd go ahead and upgrade the rear brake to the LX V-brake but, instead of controlling it with your STI brake lever, you'd make it the supplemental brake to be controlled by your stoker via her hand lever. The V-brake works here because it doesn't need a cable-stop, per se, as it's integrated into the travel agent and/or the V-brake noodle and will only need one or two cable guides on the top tube for the cable housing. Now, as for your rear brake, you have two choices:
a. Stick with the 160mm rotor and run two standard length brake cables joined using a brake cable splitter all the way to the rear disc caliper. You'd run the housing from the existing rear brake cable stop down to the rotor with one or two stick / zip-tie on cable guides. You'd also want to run the Avid's spring tension screw all the way in and add the aformentioned compression spring to improve the brake caliper's performance and feel.
b. Do everything in a., above, but if it will fit inside the stays drop a few more bucks into the rear disc to make it "better" by upgrading to the 180mm rotor ($$ for the rotor and a new Avid adapter). It still won't have the stopping power or heat capacity of the 203mm rotors -- which is the only size rotor that Avid has ever endorsed for use on a tandem as a full-time brake -- but it will be better than the 160mm rotor.
That's really about it. The "best" set-up for your '05 would have probably been an Arai drum brake mated to a really good cantilever or V-brake. But, again, having gone through the addictive bike upgrade process a few times -- usually consuming more time & re$ource$ than a factory-fresh machine would have -- I'd spend some time with pen/paper/calculator or an Excel spreadsheet running the numbers on your potential upgrade expenses before heading down that path.
A 'first tandem' is just that... the tandem you own and ride while you learn more about tandems and come to find out if it will be your only tandem or if you'll apply the lessons learned with that tandem to your next tandem.