Although the OP post is somewhat interesting it is severely flawed and frankly ill advised.
1) Removing the AUX fan just so he can install the intercooler is a mistake at the expense of his tranny. The AUX fan on the automatic transmission is design to kick in when the clutch fan is insufficient at keeping the engine in the normal operating temperature.
When your engine temperature is in the middle it reads between 167°-235.4° F. There is about a 68 degree variation between what is normal. Anyhow, when the OP engine was overheating, he was overstressing both his engine and transmission because it means that the temperature was above 235.4F. Since the automatic transmission used the engine coolant to cool down (via the tranny heat exchanger), this means that the OP's tranny was being over stressed. Any temperature above 200F will decrease the tranny lifespan and I am sure the OP just decreased his tranny life. His tranny is going to die soon.
2) The reason why BMW only install a clutch fan (ie mechanical fan) on its automatic cars is because they want to keep the tranny in its optimum operating temperature. The clutch fan is working to keep the coolant below 200 degrees so that the auto tranny doesn't get overheated. Manual transmission doesn't have a cooler and does not rely on the engine coolant to cool itself so therefore they don't require a clutch fan.