If you're going to give a bone please don't boil it first! I am a vet and cooking alters the architecture of bone, making it more likely to splinter. Raw, frozen then defrosted, is best. Ideally a scale and polish would be better still...
That's good news about the urine and I would get the crate out again.
Which country are you in? I managed to find a UK trained behaviourist in France but I was a bit lucky. I would be very dubious of the living with wolves stuff. It's completely irrelevant to dog behaviour. Ideally you want someone who is trained in positive reinforcement techniques and is up to date with scientific research on dog behaviour.
Crates are not cruel and are a source of comfort for some stressy dogs but the dog must be properly introduced to the crate. That is, leave the door open for the dog to choose to go in, make the crate very appealing (nice bed, feed in there all food, chews, etc.), praise the dog for voluntarily going in, never use the crate for punishment. Gradually you can begin to close the door.
There are more things you could be doing training wise but I am reluctant to share ideas in cases of aggression. I think your top priorities should be the vet check and then having a behaviourist over to assess the dog. Aggression is a behaviour for experts to evaluate and advise on. Don't ignore his aggressive signs though, do get someone in to help. The APBC would be my recommendation as well.
There's enough going on here to make me think you'd be better off having a good behaviourist work through this with you. Aggression in the home really requires professional input when there's this much going on. I think if you had help to understand him better it would immediately improve things for you.
If he's anxious now he'll be much worse as your DD starts to move around, and he's already resorting to aggression to communicate with you. Unless you quickly take action to change things he's going to learn that aggression is necessary.
Look up the APBC website for a local behaviour counsellor, and get your vet to refer you. The thirst and hunger may well be medical but some of the other problems are likely to be behavioural.
When you take him to the Vet get them to check his teeth as well as this may be the cause of the bad breath. Is he a small dog? Dental probs are particularly common in some small breeds.
You have to sell the crate to your dog, if he's not used to being crated you can't just expect him to love it immediately but a good way of making positive associations is to feed him in there. If you get him to choose to go into his crate that will allay your DH's concerns. It's also a good idea to do it now, before your DD is mobile so your dog has a safe place he can go to if he needs to get away from her.
Incidentally your dog doesn't understand going on the bed is 'naughty', he's a dog he doesn't have a value system. He just knows he gets told off if you see him on there.
OK you have a number of issues there which may need different approaches:
- weeing: you are right to take him to the vet, there would well be something wrong with him (may also be related to his hunger). If not, then go back to puppy training methods, i.e. out every hour, out after food/play, reward any outside toilet efforts, clean and ignore inside peeing.
- sleeps in bed: close the door so he can't go in there.
- runs off on walks: keep on lead, work on re-call, long line for a while.
- barking on lead: try to pre-empt this by getting his attention before he starts. So when you see someone in the distance he may bark at, use a high value treat (or toy if he is more toy oriented) to get his attention and turn him away from the person. Then occupy him with training (sits or downs or whatever you want) until the person is past and big reward at the end.
The aggression is something you should get professional help from someone who can come and see your dog and assess the situation. There are things you can do and they are surprisingly effective so don't panic, but it's not an issue that can be addressed over the internet as it is potentially dangerous. Meanwhile put him in a crate or the other side of a stair gate or in another room anytime he eats.
Overall he does sound stressed so he may be having a tough time adjusting to the new arrival. Try an Adaptil collar/diffuser, it helps some stressy dogs.