The system is quite complicated and maybe you try to understand the German here, only about 50 pages ;-)
training material for BMW technicians
called
Klimaautomatik IHKA (German language PDF)
and you find it here, scroll down
http://www.e38.org/e32/
There are also a lot of drawings and data to check, for example each temperature sensor in the system, how to check and which data it should show at which degree Celsius.
the control of each stepper motor is done by the IHKA control unit and it even compares the speed and things like that.
Have you checked the flap you can see from the outside when you remove in engine room the black cover at the firewall to access the blower motor?
As I mentioned some month back, the motor for the 2 outer flaps is on the driver side, and the passenger side flap is regulated from this motor too, bith with a bpowden cable. Maybe that is broken? Or just slipped out of the place where it should be?
More to check here
http://bmwe32.masscom.net/johan/ihka/ihka.html
Edit: you mentioned the stepper motor works, but did you remove the stepper motor and check if the flap is broken?