Kay I'm sorry to hear that Maggie isn't feeling herself. It sounds like she could be having the onset of an URI (upper respitory infection), I'm no expert, but from my experiences with cats, everytime their breathing sounded ruffled, or they were sneezing and stuff was actually coming out of their nose it was usually a URI. Seeing as you got her from a shelter this wouldn't be uncommon. URI's can travel fast in shelters, if one cat has it, other's are bound to get it, not all but some will. If she has a scratch like abrasion on her neck, that is probably from her scratching because of several reasons, her ears could be bothering due to a URI, or possibly being stuffed up (sort of speaking). We had one foster kitty here that scratched her neck open so bad and after a few vet visits of not finding anything, we finally took her to our favorite town vet, and Dr.Friz found that she had ear mites deep down in the ear canal, and began treatment.
Kay I would take maggie into your vet for precautions, because if it is a URI you don't want to wait any longer, if that is what she has she will need immediate antibiotics, hang in there with the proper diagnosis and possible med's, Maggie will be back to normal in no time, I'm sure of it
P.S. if you have any neosporin (the plain kind), bacitracion, or bag balm, rub some on her abrasion this will help.