Thank you for caring for these guys
. I'm hoping she is only semi-feral, meaning she has had some life exposure to humans and can get used to them again.
The only way to break the cycle is to spay the momma (she will thank you
) and socialize the kittens to be adopted out.
If it was me, I would try to trap the mom, bring her into the house (locked in a room) along with her kittens. It sounds like in time she will get used to humans. I would not, however try to pick her up or the kittens while she is around because she may indeed get angry. How aggressive has she been with you? How close have you gotten to her?
As for the box, can you put out a bigger box beside the used one and put the blanket (and the kittens) in the new box when momma isn't around? Leaving the scent for them is quite important.
Good luck!