[feltan]

Bigger cage is not a better idea. We want to make the cage their safiest place in the house not for punishment or for isolation.
Most important your dog can feel your energy. Based on your description I feel that you have a higher eneergy and dominent female puppy.
Perhaps you can start exercise her first to drain a bit of the energy before giving her training. But make sure you don't tired her over because it will lost her concerntration.
Put food and water in the cage means that is the place to eat and drink. We want to make it the cage is the best to rest and stay calm.
You already made the cage a bad experience to her, she already associate cage as isolation. I think you will need more time to change the way she feels. Don't give up. There is long way to go.
To become a happy dog owner and have a happy dog please do become a pack leader (lead your dog as a leader) and treat your dog a dog. Do not humanise them.