You can convert differential encoder signals into single endded ones with a comparator. If noise appears to be a problem I would recommend that otherwise you should be ok just running the + side of each encoder channel.
I've never used such a high resistance pot. This may allow significant noise into the signal on S1. This may or may not affect your control. I would run tests using Ion Studio with Packet Serial commands first to confirm the feedback system is working and then move to using the analog input to control the setpoint.
Low RPM can be tricky. If the motor is coggy(turn the motor manually, does it "stick" at certain angles, if so its coggy). On the other hand if the motor is relatively smooth then not running at low RPMs well could indicate PID values need to be adjusted.
The motor is ratedf for 3400 rpm. Are you using a gear head to reduce the speed? Is the 60rpm with or without a gearhead/reduction? In the case where you are direct driving from the motor(no reduction), 60rpm isnt just low rpm, it is extremely low RPM.