Everything is rigged and ready to animate except I want to add a couple more bones to my body mesh and clothes.
How do I add vertex groups for just those bones to the body and clothes meshes?
If you have done no weight painting for either the body or clothes and have the standard pose available simply parent again the armature.
If you have done significant weight painting and want to keep those weights you can lock the current weights in the vertex groups panel. Next parent again. I suggest you try this with an archived file if only to prevent some superstitious catastrophe.