The advice to separate mother from kittens MAY be good with a real feral, shy mother who stops the kittens from interacting with you.
But here the mother actively allows you to interact! So here it is NOT the case. Thus, keep both mother and kittens.
Try with Feliway if you want to throw in something extra. (google on it).
As for the Feliway, that was done almost right away. Every little advantage I can get, I'll take!
Everyone's acting today like yesterday didn't even happen. No new progress, but no regression either. Go figure. All that stressing, and I'm the only who spent the day upset.