You guys are right.
We have done away with the box and have her on a leash that reaches the middle of the room. All the dog's beds are right there and we are sleeping nearby. She has shirts and sweaters and old shoes, but she had them in her box too.
The last couple of days she has been a lot better. When I take her out at night she is very wary and slow to go, but then she doesn't want to come in. Or, more accurately, she snaps at me if I try to pick her up and she pulls hard against me on the leash. If I let off the pressure, so does she. It's a standoff. So I clip the leash and leave her in the dark, alone, and go back in. A few minutes later I go out and say "inside" and she runs up the steps and waits at the door, happily coming in.
Since she is always associating with the other dogs now, they are playing and sleeping together, she is exhibiting all the traits I'd expect from a domestic dog. Play, submission, mock attacks, and deep rem sleep, to name a few. Plus, if Bei Bei has a ball, Sandy will scheme to get it. Slowly working her way up close, Laying on her back advertising submission, circling. Very interesting to see the tension play out in tactics. If she is revved up in a game with Bei Bei, I get mock biting if I reach out to play with her too. Just hard enough to not be kissing, but not hard enough to damage me or draw blood, usually. Certainly less than the biting she gives and receives form Bei Bei. She tailors her attack even when excited. I say "nice" to her, calmly, several times and reach out slowly to touch her. "Nice". And then pet her back gently and she's out of mock attack mode and just enjoys the touch. It's clear she trusts us, we are all pack members. Then I walk away and she pounces on Bei Bei, who puts up with it to a certain point and them flattens her with a strong Alpha response. Just for a second and then they are rolling around again, deep in play. The two of them are completely bonded. Today I took Bei Bei with me on some errands for an hour and while I was gone Sandy was looking for her.
At this point, except for the night time wildness, she's a domestic dog in every way except, maybe smarter. The trusting and loving part, where she is completely vulnerable and happily puts her fate in my hands, is the most touching. In spite of the fact she's a wild thing and wary by nature and cautious, she can completely trust too. Little does she know how tenuous her future is.
In a bigger sense, all coyote futures are tenuous. But they usually win through luck, wariness, stealth, intelligence and pack coordination. In this case, and so far, she has won through luck in the beginning, and then trust. But also through a connection to human emotions that is really powerful. We see who she is, her personality and needs. How fun and honest she is.