[Nemo]

This is where you use efficiency:
OutputTorque = Efficiency*InputTorque*GR

Speed is indirectly affected by efficiency since the % of max torque will be higher in an inefficient system, which slows the motor speed. This is how you calculate it:

InputTorque = OutputTorque/(Efficiency*GR)
%Torque = InputTorque/StallTorque
OutputSpeed = (1-%Torque)*FreeSpeed

Using a blanket fudge factor isn't going to behave properly, particularly if your % of max torque is high.