For pets sake is the best vet that I know of near you. Shirly Smith from Furever gliders ( breeder and did rescue for a number of years as well ) uses that vet and lovesss them. Im not sure if she would recommend another vet over them but shed be the one to ask in that area.
https://www.facebook.com/shirley.smith6684
Thats her profile, shes also in several large glider groups on fb.
Those meds can affect their poo yes, and matted in the fur isnt that uncommon when a glider is ill or not feeling well. Take a warm damp cloth and clean it off for her then rub her fur dry with a tshirt or something that wicks moisture well.
You can give her yogurt between doses of baytril to replace the good guteral bacteria. the antibiotic affects the good bacteria as well as the bad.
As for experience with the eye, Denise Gillespie would be the person Id suggest for help with that.
https://www.facebook.com/profile.php?id=100004843098345
she has experience with a similiar eye issue I dont remember the gliders name but if you tell her the issue n tell her Carla sent you she can help more than I can with that.
I hope this helps some n she recovers soon and please try not to feel to bad, things happen and you got her the medical care she needed. Thats all anyone can do