African Helmeted Turtle lethargic, swollen eyes and sick looking?

Hello, I rescued an African Helmeted Turtle from the place I used to work at about a year ago. She had a severe case of shell rot, and the store I worked at was going to put her down. Since I have gotten her, I have cured the shell rot by taking her to the vet, and getting antibiotics and vitamin injections. Recently, she has become increasingly more lethargic, and her eyes have started to swell again. Sometimes I see mucus come from her nostrils, but she doesn't float to the top of the water like you would see in typical pneumonia cases. The vet I took her to wasn't very good, he peeled off her shell before it was ready to shed, causing her to bleed, then gave me a pamphlet about how to take care of water turtles, but the pamphlet was mostly talking about Red Ear Sliders (which eat a lot of vegetables), who eat differently than an African Helmeted Turtle (which are mainly carnivorous). She's stopped eating her pelleted food, and I mainly feed her meat, but I'm afraid this has caused her to become malnourished. She will not eat any vegetables I put in her water. She is in a 40 gallon tank by herself, heat lamp, water heater, UV-B light, lots of basking space (She prefers it) and filter. Water temperature is around 78 degrees to 80. I don't know what else to do.Is there anyone else who has had and African Helmeted/Sideneck turtle that has witnessed these problems? Also, I'm not sure how old she is, but I think she is on the older side, she is full grown from as far as I have read about her species, and I only guesstimate she is around 7 years or more. Any advice would be welcome, because I don't think my vet knows her species well at all.