I rescued two little girls last year, they had been living feral. It took Gina 8 months to let me touch her. Jenny was quicker to allow me to touch her, but only cos I spent a week up with her as she was struggling with hypothermia when we fist got her, and she was too poorly at the time to fight back, and got a bit used to being handled. Both can still lash out unexpectedly, though they are a lot calmer than when we first caught them. I guess living wild sharpened their survival instincts, leaving them much more wary of humans.

Instead of a litter box, I use an under bed storage box, lined with newspaper, half a puppy training pad and a couple of inches of hay, and both girls reliably use those.

Thank you for rescuing these two bunnies!

As Gina says, rabbits that survive going feral are probably those that have the skills of wildtype rabbits, and that means deep-felt suspicion of predators. Trusting bunnies don’t last long outside on their own.

Rabbits can be a long time before they reciprocate. My Yohio was feral, I’d say it took him 6 months to ever lick my hand. He would growl and pummel me. He still does that to people he doesn’t know very well (which are just about everybody except me). Your rabbits have each other, which makes them less dependant on affection from you. (Being a pair is very healthy for them, of course.)

Also as Gina says, a bigger box is often preferred by rabbits, and they often like to pee on soft things like fabric or hay. I used pieces of old cotton bedsheets over litter with my Bam until after a year or so when he started throwing the fabric out of his boxes, since then he just gets litter (wood stove pellets). It took quite some time to perfectly litter box train him, he was an adult when I found him and had clearly not been litter-trained.
I assume your girls are both spayed as they are rescues.