I would first make sure there are no health problems, which it sounds like you did.
I don't think your dog is being an unruly teenager. I think he just isn't properly house trained. It sounds like you are going about things right. Close, close supervision. Every time he is able to eliminate in the house, he learns that doing so is ok. You can leash him to your side if that helps. At all other times he should be crated to prevent accidents. Another thing that people always seem to forget is to reward for eliminating in the right spot. After he has done his business in the yard, give him a big yummy treat for a job well done.
As for the crate noises, all you can do is ignore them. This is part of crate training (the big bad ugly part
). If you so much as look at him while he is making a fuss, he is rewarded for the behavior. One thing I found that made crate training easier for me was stuffing kongs. This way the dog regarded the crate as a good place to be (associated it with food) and it kept him busy.
Good luck and let us know how things go