If she was born March 15, that makes her about 2 months old which is still pretty young and especially if you have only had her since May 1, she probably is still missing her mother and siblings. I think her whimpering is more from wanting or needing attention, ie. to be held and hugged and reassured that someone cares about her.

Do you have a bed for her? She may need a place of her own, where she can go and feel warm and secure. Most puppies like to have a place to nestle up in. A rug of her own, a blanket and maybe a stuffed toy or something she can snuggle up to might do the trick.