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Hey, hopefully i can help you out.
I'm pretty sure all this is going to be is your actuators didn't calibrate correctly after your battery change. Everytime you change your battery or replace the A/C control head the actuators that control the a/c doors for either the air flow or the air temp recalibrate automatically.
You can try to disconnect it again and reconnect the battery and then start the truck. You should notice the a/c system cycles all the air flow from all positions, this is the actuator recalibrating itself. Try doing that and see if it works. Worst case scenario you can always go to a dealer and ask them to just recalibrate them, they can usually do that for free if you ask nicely since it requires just to plug in the scanner and select a calibration feature.