I still have a memory of it being reported that Kidman returned to the Church shortly after living Cruise. I could be wrong!
I think she did return to the church
Tom received full custody of older two - they have had little contact with Nicole until recently
This article describes joint custody - but that the children chose to stay with dad.
Also - goes into their refusal to call Nicole “mom”
http://abcnews.go.com/blogs/entertainment/2012/07/bella-and-connor-tom-cruises-other-children/