I built the scene by using a isometric grid as a guide to create my buildings, and constantly referencing my home page to keep the style and composition consistent.
After the scene was created I made 4 loops of separate buildings so that they will have a textured cell look to them. I can then make them move up and down in Ae.
I create a comp full of these buildings moving up and down and then add the background in Ae and mask the buildings to fit the scene