Ahh I understand (I had to read through twice...)
Let her settle in at her own pace, so don't go instilling hard fast rules at this point - by that I mean, let her figure out where to sleep, let her access you at night if she needs to (if she can get to you, she's unlikely to cry or howl for you), basically be pretty easy going.
If at all possible, don't leave her alone for well, as long as it takes for her to feel secure and comfy in your home - realistically that might mean getting a dog sitter in for the first few weeks.
Treat her much like a new puppy, you don't know her routine, her communications and she doesn't know your home and your routine and how you communicate. Let all that settle in first THEN you can start to change things if you need to do that.
Bring smelly things from home. Use an Adaptil collar and plug in around the house.
Try to devise routines that make sense to her, for example if taking her for a walk - put her harness and lead on FIRST.. then put your shoes/coat/etc on.
That way she will soon pick up whether she is coming with (because harness and lead go on) or she is not (they don't) rather than getting all excited or anxious because you are all getting ready and she doesn't know if she is coming too..
Give her whatever comfort she asks for, if she LIKES cuddles and asks for those, do that - if she doesn't however, then don't. That might seem like common sense but on the one hand you have people (idiots) who believe being nice or kind to an anxious/frightened animal will reinforce fear and on the other you have those who go hysterical and giddy and clingy, and frighten the poor dog further!