If you run the window regulator all the way up for removal, the drive gear will disengage from the driven teeth. This will cause puzzlement and make you wonder if you broke it/screwed up. All you need to do is to push on the arm until it engages the gear to correct this issue.
Now, both my key in the tailgate and dash switch work. Just need to fix that slight binding issue and I'll move on to the next issue.
Congrats! One thing I noticed while putting mine back together is if you do disengage the arms from the drive gear you have to be very careful about the alignment when you put them back together. The two sides do not go in at the same point on their radius to make the channels even (and ultimately the bottom of the glass). If you are one tooth off then the window may still go up and down but the glass won't be level (and probably won't slide smoothly). Just make sure your binding issue isn't due to this potential problem.