Lots and lots of positive reinforcement, affection and using a calm, soft tone of voice with your new baby will work wonders. I once sat on my grandmother's concrete laundry room floor for 4 1/2 hours coaxing the young German Shepherd female she had rescued out from under an old cabinet. She wouldn't come out for food, but sitting there, talking to her in a calm soft voice got her to poke her head out and lay it on my foot where I could touch her.
Also, be sure to give her a "safe space" that she understands is her haven that she can go to when she is overwhelmed. And, like Brattina suggests, although she does need to be socialized, don't push her too hard right now, let her develop more self-confidence.
Keep an eye on your puppy after eating and playing, as that's usually the sequence before they have to go out. Try getting in the habit of going out with your pup and be lavish with praise and even a treat for going outdoors.
Brattina is so right about making sure she has things to do to keep her from getting bored! Border collies have lots of energy, intelligence, and absolutely love to work!