All guinea pigs breathe fast, and scared baby guinea pigs breathe even faster. But pet store pigs are often ill, so you need to watch her carefully. You need a kitchen scale (up to 5 pounds, weighs in both grams and ounces, about $15), and weigh her daily. Record the weights. She should be steadily gaining.
If the head bobbing gets worse or her head looks tilted, if she's not gaining and not eating like a pig, or if she has runny eyes and/or nose, is sneezing, or sitting puffed up in a hidey, then take her to the vet. Don't bother with a dog-and-cat vet -- they know very little about guinea pigs, and you'll likely just be wasting your money for substandard care. You need a vet that treats exotic pets -- you can click the Vets tab at the top of the page and see if there's one near you.