Direct questions demand direct answers:
1--frame material: Carbon or Aluminum
2--frame builder or manufacturer. Calfee or Co-Motion
3--brakes. Dual Calipers, with ability to fit a rear disc if you decide to go on a trip where you may find yourselves facing some challenging descents and/or riding a lot in wet conditions.
4--wheels. Lightweight, conventionally spoked wheel built around Fusion or Deep-V for training, technically challenging road courses and all other forms of non-racing w/some type of true aero wheels for TTs. Rolf's do a good job, but they're not the end-all that can do both as well as two different sets of more application-specific wheels.
5--stoker handlebars. Depends on what your stoker finds comfortable. Bull-horns are less expensive and weigh much less, but also limit the number of different hand positions that can be used. Drop bars with stoker rests (dummer levers) are heavier and have some added cost for the stoker rests, but afford a stoker all of the hand positions they enjoy on their single road bike(s).