She is a mongrel. You cannot expect her to have exact shepherd or golden dimensions. Shepherds can be quite small -- usually 22 inches at the shoulder, is minimum. 40-50 pounds is very small for a GSD, but yours is not a GSD, she is a mixture.
So maybe the litter stunted her growth. I don't think you can get that back. Check out the nutrition threads and pick a quality dog food, and start there. She may fill out some, but her vertical growth is probably done at this point.
You work at humane societies and you let your mixed breed get pregnant? What's up with that? Did the people you work with give you a good grousing at least?
Jenna, RN CGC & Babs, CD RA CGC HIC
Heidi, RA CGC
SG3 Odessa, SchH1, Kkl1, AD
Ninja, RN CGC & Milla, RN CGC
Joy, Star Puppy, RN CGC
Dolly CGC & Bear CGC
Hepzibah & Hannah