What function did the AEM have over control of the AC system?
Usually it is simply a trigger for the AC compressor clutch relay, and it could be held back by the factory HI/LOW pressure switch and AC temp sensor.
If it worked before, check to make sure the function coming out of the ECU is correct - IE is there power at the wire leading up to the connector for the AC clutch.
If you manually trigger the clutch (engine off), is the AC pulley magnetized (following confirmation that you have power headed down to the AC clutch connector and assuming a good ground)?
Confirm what pressure you have in the AC system if possible.
A few possible scenarios for you. I think this will be something simple if both ECU's control the same functions .... like a wire is not hooked up properly, etc.