Ok update time. I tore it all apart again last night, here's what I found.
First off, I am 100% certain the skipping is coming from the actuator I replaced. I put my fingers on it and turned the key, you can see and feel that its coming from there.
I am also 100% sure that the door opens freely. I put my fingers on the gear with the actuator removed and could very easily open and close the door.
I then opened up the new actuator, pulled out the gear closest to the motor to confirm that all the rest of the gears all turn freely and properly, and they do. I also reset the alignment so the notches in the shaft line up with the lines on the plastic case.
I re-assembled everything, making sure the actuator was installed properly and fully seated.
I disconnected the battery again, let it sit, reconnected, turned on ignition power, let it click away for a few minutes while I was in another room, then I went back.
End result:
It doesn't seem to click anymore. But also I still can't change from vent to floor. It feels like its stuck in between, with some air coming out floor and some vent.
What else could possibly be going on?
I also facetimed myself, phone to my ipad, so i could get a look at the gear and i took screenshots.
Any other ideas? At this point, I don't know what is going on in there. I'm tempted to reassemble the original actuator and climb under there and reinstall it just to see what happens. BUT i'm not going to do that because I don't have a garage, I had to borrow my uncles last night and it was 107° in there.
So unless someone else has another idea, I might just unplug this actuator and give up on it. Unplug because I assume even though its not clicking now, it will start to eventually.
