[JoeyP]

You've got some real good advice so far and I agree that you have a little nervous girl on your hands
She's going to tend to be passive which means she'll be afraid of new things loud sounds and new people and dogs
and this very likely came from her history

What you need to do as her owner is expose her to new things ... but you need to show her new things in a way that shows you're there to protect her and that she doesn't have to be afraid
BUT with a dog like this NEVER try to soothe her by talking soothingly and petting her when she becomes afraid .... because you'll reinforce her fear

The always wanting to be with you thing
Having her stay in her room is fine .... make sure she has her water and food and some toys
what you can do is while you are home put her in her room and let her cry a bit hover around the door and pop over and tell her what a good girl she is when she pipes down
do this occasionally to show that when she is in her room you are sometimes around

The timidity is an exposure problem
maybe she had bad experiences with men before
so what you can do is have a male friend she doesn't know come over
Tell him not to acknowledge her when he comes in
Give him a bag of treats
She will probably not want to go near him at first
But have him just put a treat on the floor a few feet away
when she takes it have him just drop a treat on the floor every few mins
Once she takes the treats without hesitation have him them hand her the treat without looking at her
after that he can let her come to him and look toward her to give her the treat
and little by little she will start to see that men do not mean "bad" things