This is the left upper arm fix. Notice the position of the bone is changed. With such a blocky mesh, the bone is best placed with the head at the top of the block and the tail centered in the joint. The vertex group is shown selected, and includes ALL of the joint vertices.
Sorry, I deleted the blend after I made the screenshots.
However, it appears that you are doing the right things, because the left arm is deforming properly. I suspect the right arm still has some overlap because the bone head is not exactly centered in the middle loop of meshes (don’t eyeball this, use the snap function – Shift+S. First edit the mesh, select the four verts and snap cursor to selection, then switch to edit the armature, select the bone head and snap selection to cursor. )