Primrose, thank you for giving a home to Toffee. You are doing so much for him, and that is truly lovely of you.
I don’t think there’s anything wrong with either one of you.
At first, he’d come right up to me and let me pet him. Now?
I can’t pick him up without him trying to run.
I can’t sit still without him trying to bite my fingers and toes.
I can’t put him down without him thrashing and kicking and fighting when we get close to the ground.
I can’t hold him without him jumping off my lap or chewing my pants.
He won’t take treats from me.
It doesn’t sound to me like he hates you, rather like he’s a little bit afraid of you, but at the same time wants contact since he bites your fingers and toes and chews your pants. Bunnies do have a tendency to try and communicate with their mouths. A bunny that wants to be pet can often bite for attention. It’s not the way people or dogs do it, but it’s very bunny-like. Same as is biting your pants, that can be an effort at getting your attention and/or trying to groom you. I recommend you wear old clothes that you don’t care so much about. My bunny Bam bites my mother’s clothes and it’s definitely not aggression but some sort of affection, but it means she has to borrow something old from me when she comes to visit or wrap herself in a fleece blankie that he can chew all he wants.
As for hating to be picked up and struggling when you get close to the ground, that is VERY typical of bunnies. Being picked up is awful for most buns except tiny babies. Being picked up equals being about to become somebody’s dinner. My buns, who are both very affectionate and come to me for cuddles, both HATE being picked up and they do struggle to get away when I’m putting them down again – so I have to have a very secure grip of their hind quarters so they don’t kick out and maybe hurt themselves.. I only lift my buns up when I have to, for grooming and clipping nails and vet visits etc.
As for taunting the dog – bunnies can be mischievous like that. Maybe he feels a bit lonely and wants to be friends with your dog? My buns want to be friends with my dog, but she’s not interested. Which is for the best I think, dogs and bunnies don’t seem to communicate very well. (Which probably is very natural since one is a predator and the other a prey animal).
Your bunny is a little too old to risk having neutered imo – he is 9, that’s an old man. Having him put under for surgery could be very risky.
I think you are having some communication problems, mostly. I’m sure others here will offer more tips on how to get a good relationship with him. It is so great that you have given this senior a home with you and it would be greater still if you and he could become best friends (your bunny probably regards you as his friend as it is, but as stated before, he doesn’t really know how to show it to you in an acceptable way.)