I can see two simple solutions:

When mirroring your geometry, your vertices on the open side didn't line up perfectly, so it ended up merging some things you didn't want it to. Fix this by selecting all the edge vertices and using the scale tool to pull them into alignment, and like GecT said, for extruding make sure Polygons>Edit Mesh>Keep Faces Together is on.


Also, your problem with the 3d paint tool painting over random stuff is because of your UVs, which are points on the model which tell the texture where to be mapped to. A simple solution is by normalizing the UVs or baking them, but that's a long and complicated process, especially if your model is at all complex.