Do you see any light green or grey bruises on the leg she favors? If there's swelling, is it worse?
You can give her a baby aspirin in the mornings and at night and that will help with the pain.
Take this time she's in the tote to train her to respond to treats. It will make it easier to handle her. Use something like dry cat food or Cheerios or meal worms, the last one being the very best treat, for the lessons. Use a verbal cue as you offer her a single treat in your hand.
Then follow that with offering the treat in a closed hand, opening it to reveal the treat. This will be useful when you need her to come to you but you haven't had time to find any treats. Keep using the verbal cue.
Soon she will come to you when she sees a closed fist and hears the verbal cue. I teach my baby chicks using this method and they are coming to me willingly by age two weeks. As they grow, they always stand perfectly still and permit me to pick them up when they hear the verbal cue. A bit of training sure makes life easier.