Welcome RDial to the board.
First off - what an incredibly sad story..with an incredibly wonderful future for this dog. You are a wonderful person.
The above poster brings up some very good points and valuable information.
As sad as it is to see your new dog yearning so desperately for affection...the best approach is to set up boundries immediately until she learns that she is safe and builds more confidence. As the poster above stated..it can take a few weeks to a few months for your dog to actually settle in so it is important that she understands where she fits in and how.
You are actually at a great advantage as you have a stable dog. He is your key to reaching her.
I suggest that you make life fun for her. Play with both dogs, go for great walks, dog parks if they can handle other dogs, hiking... By taking the dogs together, you are going to build a close bond with both dogs where she will look to him for confidence as well. Also, this should ward off any jealousy issues that I can forsee. She will feed off of his reactions to you, and you to him. She just needs to know how to be a dog and I think your boy will teach her that.
Also, I would do some one on one obedience training courses with her. Something where she has time with you, and you have more control of her. Mental stimulation does wonders for dogs..and your bond will be stronger but in a less needy kind of way.
This will not be easy at all as there is nothing sadder than seeing a once neglected dog trying so hard just to be close to you...yet you cannot give him/her that at this moment. Best advice is to be confident and upbeat with your dog. This will instill some confidence in her.
Best of luck and thank you so much for saving her.
Stick around as there are some wonderfully knowledgeable people here on pets that can give you some ideas, tips and further advice.