I am so sorry you are experiencing this and so sad about the loss of her sister!! Sadly that's the fate many many puppy store dogs suffer, they're crammed together at a crucial time in their lives - heath wise, and pass around sicknesses so easily. Gigi is incredibly lucky to have you... I've read so many stories about people not willing to pay for all the medical treatments their puppy store dog usually needs after they buy them!
Your biggest asset will be a vet with is familiar with the EB breed! It sounds like you have a thorough one now, since they spotted the megaesophagus and the loose kneecaps.
good luck to you and your baby through this, it doesn't sound as though she's doing awful, and I hope you see improvement asap. I've dealt with kennel cough several times but it usually cleared up in a few days and never progressed to pneumonia. it's so much easier for the younger ones to get worse sadly. keep us updated!