Stepper Motor Voltage
Darlington pairs have very high saturation voltage. 
In this case if you refer to the datasheet for the TIP122 you will see that you might expect anything from 2-4V across the C-E. 



In your case the saturation voltage will be very high because you have minimal base current for the TIP122. 

A FET may be a better device to consider. 

Update: The base current you use is far too low. You have to overdrive the base to ensure the final transistor gets closer to saturation. 

Using the Fairchild datasheet for the TIP122 (there is an error in the OnSemi version) you get this graph. 

 

For Ib=Ic/250 you will need 4mA of base current (it's slightly more complicated than this because of the internal resistors). With a Vbe(sat) of around 1.5V you need an 875 Ohm base resistor driving from a 5V Arduino.   

This should give you a Vce(sat) of approximately 0.8V at 1A.