Hi Shelby,
Maybe now I sorta halfway understand what you are trying to do.
What I don’t know, is how messy the Geometry actually is, and how assigning different Materials in Fusion would be easier than in Blender (due to my lack of knowledge of Fusion). You also don’t need to Separate parts to give them different Materials; that might be part of the problem why Copy Materials to Selected doesn’t work.
What I do, when a Mesh is messy, is to re-Topologize it. That saves me so much trouble, whenever I need to do anything at all with the model. But I gather you don’t want to do that (a lot of people don’t like re-Topologizing).