Chiming in here, my experience is not with pups but with neonates.
While its possible that you might have a PDA, I've never run across one that was that loud on its own. To become that loud, there is usually another defect present such as an ASD or a VSD or some type of stenosis. The lack of weight gain is a concern because it suggests the defect is severe enough that she can't meet her metabolic needs and have enough energy left over to grow.
Is there any way you can get her in to a specialist? They really need to do an ultrasound and chest xray on her to determine the underlying cause and best course of action.
Here are a few sites I've found to give you some more information.
Signs of Heart Disease in Dogs Heart Murmurs in Dogs | petMD Heart Murmurs in Dogs | The Veterinary Expert| Pet Health
Good luck and thank you for helping these puppies.