Hello. I know exactly what u are going through! I have 3 indoor cats of my own and in Feb, I coaxed a pregnant stray in (knew there was a blizzard on the way and was worried about her giving birth in the blizzard).
Before I could get her to a foster mom who's very experienced with pregnant cats, she gave birth to 5 kittens!! When I tried to put her in the cage to take to the foster home, she freaked out, attacked me and hiss like crazy so I gave up. I am SOOO thankful that none of the kittens died- I don't know if I could have handled that!
During the first week, when I tried to look in the box to see how the kittens were doing, she'd growl/hiss and swat at me but after I spent time in the room doing my own thing and each time getting closer to her and the kittens, she got used to me and let me pick the kittens up to hold/pet them.
Try that and also try what HIssy suggested regarding the sponge & smelly clothing.
Now they are all about 7 wks old and driving me nuts! 4 out of 5 have conjunvitis so I have been driving myself crazy and getting plenty of wounds while dosing them with medience!
Hopefully, the infection will clear up within 2-4 wks so I can go ahead and give to interested families. I'm keeping one kitten (she's the runt of the litter but is the most hyperactive of all!)
So, I know what it's like!