I got Ivy from a rescue (puppy mill ) last July. and she is still shy. She loves me (I can't go anyplace without her at my feet) but maybe because she is about 5 years old she will never act like a dog you get from a puppy
I wish I had some of your problems I think that can be taken care of easer than the shyness and the fear. Good luck and keep us updated I would love any ideas you have about how you get your rescue to fit in.