Most go to a shorter stack to move the powrband further up. The factory stacks are pretty long to begin with, and too my knowledge there are no other factory style, rubber stacks that are longer and readily available.
The interior of the box is just that, a box. There is no easy way to change the chamber volume like on the gen 1. I did a box for a previous bike of mine and lessened the chamber volume by adding material to the interior of the box and smoothing the radiuses of the box. This wasn't easy by any means and required ALOT of time on and off the dyno.
If you want more lower and mid range torque, look into going with an ecu flash and have a reputable tuner adjust the bike for you. Ignition timing is what makes power and torque. Fuel control is just for thermal principles and detonation deterrence. Adding a pipe etc will not effect low end (rpm) performance, but mostly affect the top end of the rpm sweep. IF you want the presence of torque per traveling mph, gearing is the cheapest means of doing this. But, if you're touring at spend lots of time at highway speed, adjusting your effective f.d. would be detrimental.