Hi Cadbury,
Anyway, the custody is under a care order at the moment
which means that he is being monitored by social services?
I'm not sure that you taking out an injunction against him (presumably to stop him harrassing you?) would affect how social services see his caring for his son. They are responsible for his son's welfare - and his treatment of you may not be taken into account. He might harrass you, but if he's ok with his son, that's all that will matter to them.
And if his son is okay, that's all that matters. If his son was taken into care - meaning a care home or foster parents, who knows what might happen to him? He could well be better off where he is. If he's not being sexually abused, beaten up etc, then consider what might happen to him 'in the system'.
If you are concerned about his son, could you (do you) attempt to keep contact with the son? Can you offer to take him out, have him stay with you....etc?
Portia