A few people have emailed and PM'd me about how to connect the geared stepper supplied by Bondtech with the QR extruder. Also, Kysan 1040229 geared stepper is popular and is the stepper I use with my QRs since I had a few of them already. After a bit of research and email exchange with Martin at Bondtech, I put together the following chart:
Phase Kysan Stepper QR Stepper
1(A) Red Red
1(C) Green Gray
2(B) Yellow Yellow
2(D) Blue Green
With any 4 wire stepper it is easy to find the two phases. Here are two simple methods:
Make sure none of the wires are touching and spin the shaft of the stepper to feel how much resistance there is. Now, connect any two wires and spin the motor shaft again. If it is much harder to turn, you have identified a phase! If it has about the same resistance to turn as when unconnected, connect one of the connected wires to a different wire and test again. Once you've identified one phase, connect the other pair of wires and verify that the motor is harder to spin. That is the second phase.
If you have a volt meter, set it to measure resistance. Then hook up any pair of stepper wires. If you measure any resistance, you have identified a phase. For the Kysan stepper, the phase resistance is about 2.4 Ω. For the Bondtech stepper, it is 1.7 Ω.
Once you know which pair of wires form a phase, you simply connect them to your control board matching the phases. You don't need to worry about which phase goes where as long as you have the phases connected properly. A simple firmware change (to change stepper direction) is all that's required if the wires are hooked up reversed so it is much easier to just hook the stepper up and deal with it in firmware.