I agree with Baby Yorkie that I prefer scratching to barking.
While a face scratch isn't pleasant, I would be pleased if my dog was waking me to go to the bathroom instead of doing it in the house.
Maximo grunts politely in my ear to wake me up. Not sure how to train a dog to do that instead of scratching. How about training him to use a doggy doorbell? You could keep it in your bedroom and train him to ring it. The bell comes with instructions for training. Some people use simple jinglebells or windchimes strung to a doorknob.
For general jumping and scratching, train your dog to "sit" or "down." Then if he jumps up on you, give him the sit or down command.
I would ditch the water bottle spraying. He may think it is a game in these instances, or he simply isn't perceiving the spray as meaning "stop what you are doing."