I live in an apt with hardwood floors, too, and my bun loves running around on the rug. It’s not shag; it’s short with a dense, but soft texture. In his cage, I have his corner set up with litter where he goes to the bathroom, and I have the rest of the cage filled with Timothy hay and that seems to be comfortable for him. I also have a runner that has like a straw-like material woven in, so it’s very sturdy and not plush at all and he seems to like the way that that feels on his feet. Lastly, I keep an ottoman next to my bed so that he can easily hop up and hang out up there if he likes. When I moved in, my first priority was to find rugs! That hardwood is so difficult for him to run and play on, but a nice rug with a firm feel to it is perfect. Hopefully that helps.

The blanket in her crate would be better for her than her grass mat. I would consider taking it out for a while and seeing if her foot shows any improvement. As for how to treat it, some plain neosporin and possibly a gauze wrap should help keep it protected

You could try a bathroom memory foam mat.