Fixed it! It definitely was that extra face I had floating around in the background. Forgot I had changed the belly button a bit and didn't weld the UV's there. Changing it messed with the vertex order and caused some difficulties, but I managed to save my sculpting job. Everything is great! =]
I'm kind of confused with what you're doing to be honest. Subtools would have their own independent UV sets, and baking only cares about the active subtool and its subdivision levels unless you're using MME with the subtool option turned on. You shouldn't even need to copy and paste UVs, just export the tool, change the…