Let's back up a minute...
You said you replaced the mode actuator because of "popping noises." This is pretty typical of one failure mode of those actuators. The center drive gears are crappy plastic things that eventually crack. But then it often results in the position sensor (on another plastic gear in there) getting out of whack so that BCM doesn't "know" where the door is so it closes it down.
a) How did you know the popping was the MODE actuator? Right above that is the defrost door actuator. More or less next to it is the temp control actuator. Two other actuators with the same cheap, crappy, plastic gears.
b) Before the replacement was it blowing out the face?
For now, don't disconnect the battery. There is no need for that. But pull the HVAC-B fuse (I forget the # - look on the diagram) for like 30 secs. Plug it back in. Start it up and don't touch the HVAC controls for a good 1.5-2 mins. See what happens.
This is probably not going to help, btw, but is a place to start. The reason I think it probably won't help is that you said it worked after you first replaced the actuator. What we still don't know is whether it worked BEFORE you replaced the actuator.
Mostly you need the codes. Like I said, it has five wires. That's a lot of failure modes. (There's a constant 12V signal, a 5V ref signal, a position signal, a 5V control...)
When you had the actuator off, did you happen to flop the door around by hand, and if so, did it move freely?