This guy has a nice calculator that works, simple too
www.rickwrench.com/bunchofcalculators.html
X pipes don't work on twins as the pulses are too far apart to mesh as they do in a V8.
The small pipe on the Ninja250 H layout is called a balance pipe. It is too small for scavenging but I can't remember if it was for noise or emissions ......
Beatr911 that link at dairally looks deep, i cant wait to try it out !
On the carb switch, 1 single carb usually gives better low end torque while separate carbs perform better at higher RPMs.