Wow sounds stressful!!! Hope you guys have recovered. Can DH give DS a special bear (maybe make one) to cuddle when he is not there? Maybe explain it and make a big deal? It has often taken a while to settle into new routines and sounds like you have had a few big changes all at once.
I have just put both kids in with me but it took a while for the older one to get in the swing as she was pretty jealous of DD2.
xxxxxxx