It sounds like you are doing a wonderful thing for this bun. That's great that the poop problem is clearing up. Diet often makes a big difference in a rabbits health. I'm sure it was wonderful to see her take those steps. It sounds like she has the capability of possibly regaining some mobility back. Has your vet prescribed anything to help with your buns arthritis?
A rabbit with a disability doesn't mean it should be put down automatically, so I'm glad you decided against it. As long as she isn't suffering and is happy in herself, with the proper care she can still enjoy her life. You may want to check out these sites for disabled buns(if you haven't already). They have some good info on how to care for buns with disabilities. I know that some rabbit owners have devised slings for their buns with hind limb weakness, to support them so that they can help the bun walk and build those muscles back up. May be something to look into.
http://www.disabledrabbits.com/
http://www.hopperhome.com/Disabled%20Rabbit.htm
http://www.catsandrabbitsandmore.com/disabled_rabbits
The grunting was just a warning as your bun was probably just unsure about your cat, but was fine once she realized your cat just wanted to snuggle. They may even become best buddies. I've read of other buns bonding with cats, so not unheard of
Here is one good veggie list for rabbits.
http://www.lagomorphs.com/salad.pdf
ETA: The poop clusters, or cecotropes, are normally eaten by rabbits directly from their bottom. Sometimes an occasional one will be left by a bun and sometimes diet or medications can cause a bacterial change in the cecotropes and so a bun won't end up eating it because it doesn't smell right. But uneaten cecotropes can also happen because a bun has a health problem like arthritis, and they can't reach down there to eat them properly. So if the cecotropes aren't mushy and seem formed properly, if you see one left uneaten, you may want to offer it to her and see if she will want to eat it, in case she just couldn't reach it to eat it herself.
http://www.therabbithouse.com/diet/rabbit-droppings.asp