The solution was to put them on a separate layer, hide the existing clothes and just skin the pyjamas on top of the full rig. Then add attributes to the main character control which allowed the visibility of the clothes to be turned on and off as needed.
I have added a few attributes that control the visibility. 'Clothes' is the usual outfit. We will then later turn this off and turn on 'pyjamas'.
Normal clothes and 1940s hair
In regards to our other character who represents the start of the 1950s this would have been a completely different character but he is very similar except the texture of his clothes, his face shape and his hair. So we are going to use the same clothes but a different texture map, blend shape his face so he just slims down a bit and like the change into pyjamas for the first character I have added a visibility control for the different hair styles.
Now all I have to do is re-skin these elements :)