There are no computer tricks. You find the neutral safety switch, locate the ground wire (check your Bentley, and if you don't have a Bentley, or BMW tech manual, you shouldn't be doing this in the first place) The ground is not hard to locate, it's the brown one, and run it to ground, just that simple.
The auto ECU is out of the loop at this point, it is doing nothing and controlling nothing, has no effect on the car at all, does not communicate with the engine DME on an OBD1 car, just reads data from the car (basically, RPM, transmission status, and road speed), and regulates shift points and communicates faults via the dash, and can go into limp mode. Pretty dumb computer, and none of its functions has any bearing on a manual transmission.
You can retire it in place, or remove it, whatever you'd like, though you might trip a fault light on the dashboard, which is a two minute job to disable by plugging the light socket. I wouldn't recommend trying to take the trans harness out, it's sort of integrated into the entire harness, just cover up the exposed sockets and let it be.
As far as the reverse lights, you'll need a manual trans reverse light switch, which is in located in the center console.
Basically when the shifter is moved into the reverse gate, it pushes a contact in, completing a ground and turning on the lights. You have to locate the old automatic plug, which connected inside the transmission tunnel, run about two feet of two conductor wire to it, and splice into the ground and power leads. Shit simple to test to see if it's working.
Hardest part is routing the wire, insultating it and tucking it up out of the way, thats why I suggested you do that first, rather than last like we did, it'd be a lot easier if the trans and driveshaft were not in the way.