Did he have a dog house in his run? I would try a crate with a nice soft rug or blanket to simulate a den or his dog house.
Watch you energy. He sounds more like he is trying to dominate you. He has you getting up at night. :)
Assuming that he is just insecure in a new situation, you need to set boundaries, limits and rules for him and enforce them firmly and in a calm assertive manner. You might loose some sleep until he understands he sleeps in his crate in the kitchen or laundry room or wherever you decide.
When my boy comes and nudges me for attention I growl at him to "go lay down". (I have a different command for when I want a down or down stay) He looks submissive and goes and lays on a throw rug I put in his favorite spot. After he has been laying down for awhile, or I have finished what I was working on, I will call him to me and give him some attention.
If you haven't taken Cesar's Sessions, I recommend them. His book, "Be the Pack Leader", is very helpful also.
He shall be everything humanity strives to be: Honest, Loyal, Kind in Heart, and Strong in Spirit. Therefore, you shall call him Partner and Best Friend."
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