Thanks for the reverse engineering of the motors! I found two of these mountings partially disassembled in our institute's garbage today and at first I had no idea what kind of motorized gadget it was. In these particular units 2 PIC microcontrollers powered from a single 20 MHz quartz do the control of the two motors, the rest of the assembly looks identical.
I assume though that the direction of rotation is not simply output by the encoder on the motor - normally these encoder give out a quadrature signal, i.e. both channels pulse once for each tooth on the wheel with a timing offset which indicates the direction of rotation. BUT yes, you are of course right, the HOA902-11 on your mount has an integrated quadrature decoder which is absent on my units, there is only a normal 2-channel IR receiver.
I would never have thought of using DC motors, but for ages I had wanted to motorize my own Tasco parallactic mount - and now with these motors and a 3D printer it might become a reality, more than 30 years after I got my telescope. I will probably not follow the rest of your project, but rather develop my own driver circuit and software, but thanks a lot for sharing so far!
Uwe.