How can I reduce the size of the animation?

You might want to put a Null Object as the parent of those three elements, then just adjust the scale of the Null Object. Elements take the properties of their parent (Null Object) except opacity.

Shrink how? Your screenshots are mostly useless since you did not select the layers and cropped out the timeline, so we can't really know what's going on, but it seems like you are blindly chnaging the scale values of soem shape layers without having adjusted their anchor points, either of the layers themselves or the shape groups contained in them. Since scaling is realtive to the anchor point of course it will be different if those are not aligned properly. And I suppose that's basically your answer. You need to group the shapes consistently and adjust the anchor point and/ or pre-compose the layers and scale the resulting new layer in the parent comp.

Mylenium