since gears multiply torque...
 

then how come we adjust dynos when we get them put in? If we left the dyno to assume stock gears, wouldnt it show a torque increase on the graph? Or am I missing something?

Gears dont change torque, they multiply the torque through the drivetrain, there is no gain in power, just the way it is put down. Kinda like using a long lever to get more leverage.