Since IAT is built into the MAP sensor on this engine (isn't it?) then IAT error could be due to the unplugging game. Clear up the errors and recheck. With the stepper though, well, either it's gone, or has wrongly connected wires. It takes 4 I think, two for each two coils, and sometimes (from motor to motor and from loom to loom) this can be messed up, at least a problem like that was at least once reported on Centomania in PL. Any further details of this error on your tester?
EDIT: Also, non-functioning IAT would not have that big influence on the runnig, when it is gone a relatively safe value is substituted, and the fuel dose would only be very slightly off from what it should be. In other words, concentrate your efforts on the stepper motor
EDIT2: Another thought is, the error codes of this tester do not tell me anything, but I would also keep in mind that the "stepper error" could be concluded by the ECU from the inability to keep idle. This as we already discussed does not have to be due to a fault stepper per se, but wrong fueling too. First check would be to clear the errors, turn the ignition off then on, without starting the engine, and then check for the WL, and it on, read the codes. If the stepper error is reported after clearing and without starting the engine then it is the stepper itself that is wrong.
EDIT3: Perhaps too obvious, you did check that there are no leaks in the inlet, right?