Loss of freedom is the most severe punishment, so remember this when you want to hold a bunny that wants down. The good news is that a spayed or neutered bunny will chew less and less as they mature. If all else fails, try bitter agents in a pump, sprayed onto chewed areas. Just spray it on the furniture or objects just before she chews them. The catch is that it wears off very quickly, so you have to be waiting.
Rabbits are very easily litter trained.
First, get your rabbit used to going to the bathroom in the cage, then gradually give access to the house in small increments. Place a cat litter box or pyrex baking dish with litter in the corner of the cage where the bunny prefers to urinate. Place some droppings in the box and reward the bunny every time the litter is used. Punishment has no place in housetraining. You may also wish to place a food bowl just next to the litter box since they usually pass stool while they are eating.