You mentioned you did have your your yorkie in your room....
Thats where we have Sophie...she cried those first nights off and on...and if you are right near and speak to her...
I would put my fingers in the front and Sophie would lick them..and settle back...
Sounds like your puppy is lonesome and needs to feel connected to you.
And maybe the barking is also wanting to go out at 2 a.m. like you used to do~ (just a thought)
I put Sophie in her jammies..she knows its bedtime...like everything else..we have a little routine...nothing changes..always the same...she seems to like that.
I'd do something and stick with it and not move her from room to room...
You may need to start all over and let her back by your bedroom...only a few days consistant..and she will develop the routine...(promise~)
Good luck to you...oh..and make her crate as comfy as you can....
Sophie has a nylabone, stuffed animal, fleece bed, and blanket to cuddle with...she kind of likes settling down for the night.
Let us know how things are going....