The key to getting everything to line up in the camera view in After Effects was to create a master shot. That shot would be on top of the stack of layers I imported from Photoshop. In After Effects I could set the blend mode for the master shot to Difference. With that setting the frame would turn black whenever all the layers were perfectly lines up. With my drawings it became even more convenient since they would be visible as light lines.
In this shot, I believe I am trying to scale the foreground people into position. When a layer is pushed back in space it appears to get smaller in the camera view. It then has to be scaled back up to size and lined up with the master shot. Since several versions of the foreground characters are visible they haven’t quite lined up yet. When lined up everything turns a rich black with only lines faintly visible. I will probably be using this effect in all 162 shots.
Ideas for pandemic themed paintings keep popping into my head, but they will have to hold until I wrestle this film into submission.