It has to do with the motion, not the motor, therefore you'll have to make adjustments and reset it to learn the end stops regardless of which direction you travel.
so, the absence of flaps will cause the bar to revolve infinitely, even with your motor attached.
remove the flaps and bar, replace the manifold and then find a place to reset the modifications. ISTA isn't required; autel, launch, and others can accomplish the same.