Welcome to an issue us DS4 users have had since autofit was launched.

The shoes themselves are the problem, many of them were not built around V4's zero'd foot pose, so changing the rig to V4WM (or Genesis) means they will never conform properly. You either need to create a new .OBJ after posing the shoe so it fits V4's zero'd pose and then rig that mesh, or turn them into props and lose the rigging.