It sounds like you’re doing everything right, and brushing just has to continue. Don’t be afraid, but if you are gentle, be more frequent. Just give her a small treat and pet her as you do it so it becomes a pleasant bonding thing for her. It will help her get through the shedding, when they do tend to become more ornery than usual.

The reddish pee is nothing to worry about as far as I can tell right now, especially since you asked your vet who knows her personally.

You want to make sure she eats a lot of hay, and can try fresh pineapple, papaya tablets, and plenty of water to keep her gut passing the pearls. If they continue you might have the vet check her for early signs of a blockage, but so far I think she just needs some help to keep the hair out of her tummy. Also, try to vacuum her area, around the house, and use a wet glove or paper towel to pick up loose hair. It’s floating around her stuff so she can ingest it that way, too.

That’s good that the fur is passing through – that means that her gut is working – brushing as she can tolerate it is good as well. Red/orange urine is perfectly normal for rabbits.