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So if you were a client, my thought would be to try doing counter conditioning definitively. Remember counter conditioning is: conditioning in order to replace an undesirable response (such as fear) to a stimulus with a favorable one. So making it about you coming towards him when he is quiet does nothing for his association with being the kennel itself. What’s in it for him? If it’s you coming closer, that can be counterproductive.
I’d ask the following before starting a plan: how big is the kennel? Is it soft and comfy? Is there water? You mentioned the longer he runs the worse it is….water? and can he stretch out? is it too hot in the kennel?
If the responses are favorable I would suggest starting counter conditioning by making the kennel a place he goes to enjoy things like: chewing, napping, eating snacks (frozen almond butter in kongs, fish sticks, a smear plate etc). Playing relaxing music and a lavender rubdown really help some of my client dogs (young living lavender EO).
To overcome the separation part have him in it when you are just hanging out in the same room, make it apart of his daily routine whether you need it or not.
He knows the kennel makes him vulnerable , keeps him away from his favorite person. Another thought: a lot of the barking can be barrier frustration. So making the kennel a nicer place can be helpful.
The chain link fence I would do phase 3 leave it, recall, or this way. Once he realizes that every time there is a chain link fence, dad gives him a command to do something else, he will realize that that interaction does not serve him AND making it about obedience rather than punishing an emotion with ensure he isn’t afraid of or building a negative response to fences, and will nurture your relationship first training plan.
